Full wwpdb NMR Structure Validation Report i
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1 Full wwpdb NMR Structure Validation Report i Feb 12, :13 pm GMT PDB ID : 2KH2 Title : Solution structure of a scfv-il-1b complex Authors : Wilkinson, I.C.; Hall, C.J.; Veverka, V.; Muskett, F.W.; Stephens, P.E.; Taylor, R.J.; Henry, A.J.; Carr, M.D. Deposited on : This is a Full wwpdb NMR Structure Validation Report for a publicly released PDB entry. We welcome your comments at validation@mail.wwpdb.org A user guide is available at with specific help available everywhere you see the i symbol. The following versions of software and data (see references i ) were used in the production of this report: Cyrange : Kirchner and Güntert (2011) NmrClust : Kelley et al. (1996) MolProbity : 4.02b-467 Percentile statistics : v01 (using entries in the PDB archive December 28th 2016) RCI : v_1n_11_5_13_a (Berjanski et al., 2005) PANAV : Wang et al. (2010) ShiftChecker : trunk28760 Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et al. (1996) Validation Pipeline (wwpdb-vp) : recalc28949
2 Page 2 Full wwpdb NMR Structure Validation Report 2KH2 1 Overall quality at a glance i The following experimental techniques were used to determine the structure: SOLUTION NMR The overall completeness of chemical shifts assignment was not calculated. Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in the following graphic. The table shows the number of entries on which the scores are based. Metric Whole archive NMR archive (#Entries) (#Entries) Clashscore Ramachandran outliers Sidechain outliers The table below summarises the geometric issues observed across the polymeric chains and their fit to the experimental data. The red, orange, yellow and green segments indicate the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A cyan segment indicates the fraction of residues that are not part of the well-defined cores, and a grey segment represents the fraction of residues that are not modelled. The numeric value for each fraction is indicated below the corresponding segment, with a dot representing fractions <=5% Mol Chain Length Quality of chain 1 A B 254
3 Page 3 Full wwpdb NMR Structure Validation Report 2KH2 2 Ensemble composition and analysis i This entry contains 77 models. Model 1 is the overall representative, medoid model (most similar to other models). The following residues are included in the computation of the global validation metrics. Well-defined (core) protein residues Well-defined core Residue range (total) Backbone RMSD (Å) Medoid model 1 A:1-A:153, B:1-B:110, B:129-B:254 (389) Ill-defined regions of proteins are excluded from the global statistics. Ligands and non-protein polymers are included in the analysis. The models can be grouped into 11 clusters and 9 single-model clusters were found. Cluster number Models 1, 3, 7, 8, 15, 16, 17, 19, 20, 21, 24, 25, 29, 33, 42, 1 55, 58, , 31, 35, 37, 39, 40, 48, 56, 62, , 57, 64, 67, 68, 71, 74, 75, , 12, 30, 34, 43, 46, 59, 70, , 11, 22, 38, 54, , 14, 49, , 50, , 4, , , , 63 Single-model clusters 13; 18; 26; 28; 32; 51; 52; 73; 76
4 Page 4 Full wwpdb NMR Structure Validation Report 2KH2 3 Entry composition i There are 2 unique types of molecules in this entry. The entry contains 6250 atoms, of which 3099 are hydrogens and 0 are deuteriums. Molecule 1 is a protein called Interleukin-1 beta. Mol Chain Residues Atoms Trace 1 A 153 Total C H N O S Molecule 2 is a protein called scfv. Mol Chain Residues Atoms Trace 2 B 254 Total C H N O S
5 Page 5 Full wwpdb NMR Structure Validation Report 2KH2 4 Residue-property plots i 4.1 Average score per residue in the NMR ensemble These plots are provided for all protein, RNA and DNA chains in the entry. The first graphic is the same as shown in the summary in section 1 of this report. The second graphic shows the sequence where residues are colour-coded according to the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretches of 2 or more consecutive residues without any outliers are shown as green connectors. Residues which are classified as ill-defined in the NMR ensemble, are shown in cyan with an underline colour-coded according to the previous scheme. Residues which were present in the experimental sample, but not modelled in the final structure are shown in grey Scores per residue for each member of the ensemble Colouring as in section 4.1 above Score per residue for model 1 (medoid) T147 M148 R4 S5 N7 C8 T9 2 D35 Q38 Q39 M44 V47 Q48 K55 C71 V72 L73 K97 I104 E111 F117 P118 T124 K138
6 Page 6 Full wwpdb NMR Structure Validation Report 2KH2 G241 S M163 P K194 Y223 Y224 T5 L11 7 R18 V19 T20 I21 W35 Q38 K39 K42 K52 G64 S65 S67 G68 T72 L73 N85 F91 W92 3 K107 R Score per residue for model 2 T9 2 D35 Q38 S45 E50 D54 P57 C71 D75 S84 V85 E105 N107 E128 A226 R227 Y237 W238 Q132 S P I2 T5 Q6 S7 L11 T22 S26 G27 N28 N31 Y32 W35 Y36 P44 L46 L47 V58 P59 T72 L73 I75 S76 Q Score per residue for model 3 R4 2 A28 Q32 E50 D54 P118 T124 7 W35 L46 L47 N50 D56 G64 S65 W92 3 L140
7 Page 7 Full wwpdb NMR Structure Validation Report 2KH2 62 M163 S164 W V A226 R227 H Score per residue for model 4 S5 2 Q32 K55 N89 F99 I104 W120 Y121 I122 M S M163 P Y224 K231 M4 L11 T20 I21 R24 T72 L73 S77 K107 R108 L Score per residue for model 5 R4 S5 2 L29 Q32 K93 K94 N107 E113 Y121 T124 T147 M148 F150 Y237 W238 S129 E130 V131 Q132 L133 6 M163 L208 Y209 Y224 I2 Q3 M4 T5 T20 K39 A43 P44 N50 A51 K52 A84 W92 3
8 Page 8 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 6 2 M20 L31 Q32 M36 V40 S52 K55 I56 C71 S84 F99 K103 I F150 S F197 N213 4 R227 W35 S67 G68 N85 Y86 Y87 Q Score per residue for model 7 T9 Q32 D35 V47 D54 K55 I56 S84 V85 K103 I104 E105 N107 Q116 S129 E130 S154 G155 F P170 G171 G183 G184 A221 A226 R227 7 S26 D56 E105 R Score per residue for model 8 L31 D35 M36 L73 S84 V85 F99 E105 F117 P118 T124
9 Page 9 Full wwpdb NMR Structure Validation Report 2KH2 S F158 S159 P A226 R227 T5 T20 R24 Q38 N50 A84 F91 F98 S129 L Score per residue for model 9 2 L29 Q32 S45 A59 N89 K93 K94 E113 W120 Y121 I122 K138 Y237 W R F197 D219 Y224 A226 R227 T5 Q6 S7 T20 A43 P44 K52 T53 L54 S65 I75 S76 P80 N85 Y86 Y87 W92 K107 R Score per residue for model 10 2 G22 E25 V47 K65 N66 C71 S84 V85 K93 K94 K97 L133 6 S M163 L208 Y223 Y224 G241 S248 S T22 S26 I29 N31 Y32 S67 G68 S77
10 Page 10 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 11 D35 N53 C71 D75 S84 V85 N89 S P170 G171 P A221 T5 T20 I21 T22 S76 Q89 F91 R Score per residue for model 12 R4 T9 2 L31 M36 K55 L73 S84 V85 N107 F117 Y121 I122 F150 V151 S M163 D202 N206 Y209 Y224 L11 S R18 V19 T22 T53 L54 S67 G68 I75 S76 K107 R Score per residue for model 13 T9 2 S52 K55 C71 K74 D75 N89 F99
11 Page 11 Full wwpdb NMR Structure Validation Report 2KH W165 V R216 I21 T22 S26 L73 K107 R108 P Score per residue for model 14 S152 P2 V3 R4 S5 T9 L31 M36 S45 F46 G49 E50 E51 S84 V85 K103 I104 E111 T124 P131 F150 V151 6 S F158 S M163 Y224 T5 S26 Y36 P80 3 S Score per residue for model 15 T9 A28 L29 V47 I56 C71 V72 L73 S84 V85 N89 F99 K103 F117 P118 L F158 S159 P N206 S12 G16 V19 T20 I21 T22 W35 Q38 K52 I75 S76 S77 A84 K107 R108
12 Page 12 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 16 R4 S5 T9 2 E50 N53 I56 K93 K103 I104 E105 N107 W120 Y121 P131 A226 R227 S248 H249 S129 L133 V134 E135 P143 C S154 G155 F M163 G183 P M4 T5 Q6 S7 S26 Q38 L46 L47 N50 A51 K52 T53 D56 S63 G64 S65 T72 S76 N85 Q89 F98 G Score per residue for model 17 R4 S5 T9 2 M20 V40 F46 V47 Q48 K93 K94 E S129 E130 V131 E135 L S154 G155 F M163 F197 S10 L11 7 I29 Y32 L46 L47 N50 V58 P59 S67 Q89 F91 W92 3
13 Page 13 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 18 V151 S152 R4 S5 2 M20 G22 E25 L29 Q39 N53 2 K65 C71 S84 V85 K93 Q116 T124 S125 M130 K138 T147 M148 F150 D202 N206 Y209 S248 E135 P F M P170 G171 G183 G184 F197 S7 7 R18 V19 T20 I21 T22 Q37 Q38 K39 K42 L46 L47 N50 T53 L54 I75 Y87 W92 3 G101 K Score per residue for model 19 2 D35 Q39 C71 E113 P118 W120 Y121 I122 S M163 R F197 D219 A226 R227 Y237 W238 V19 T20 I21 T22 W35 P44 L46 L47 G68 L73 I75
14 Page 14 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 20 2 M20 L31 D35 M36 V40 K55 S84 V85 F99 I104 E105 N107 T147 L M163 S164 V177 K194 N206 N213 4 W238 T5 K39 K42 A43 P44 L46 N50 S Score per residue for model 21 R4 S5 T9 2 Q34 Q39 E50 D54 K55 L73 S84 V85 I104 E105 E111 T F146 T147 M148 D219 Y224 Y237 W238 S129 Q M163 S164 F197 E218 I2 S7 S12 7 R18 V19 T20 W35 Y36 Q37 Q38 P44 L46 L47 K52 G64 S65 I75 P80 N85 F91 W92 3 E Score per residue for model 22
15 Page 15 Full wwpdb NMR Structure Validation Report 2KH2 G22 E25 E50 K55 C71 V72 L73 S84 V85 N89 F99 F117 P118 T124 T147 M148 F150 V151 S152 S K194 F197 N206 I21 N31 Y32 L46 S63 T72 L73 F91 F98 R Score per residue for model 23 A28 L29 Q39 S43 N F197 A226 R227 Y237 T5 L46 S63 S67 G68 Q89 Q Score per residue for model 24 V151 S152 S5 T9 2 Q14 Q32 G33 Q34 D35 M44 E50 D54 K55 V58 V85 K97 V100 F101 K103 N107 P131
16 Page 16 Full wwpdb NMR Structure Validation Report 2KH2 H250 S F158 S N206 N213 4 K231 L232 T5 S12 3 V19 S26 W35 N50 A51 K52 G64 S65 I75 S76 F91 K107 R Score per residue for model 25 2 Q14 Q15 M44 E51 S52 K55 I56 P57 L73 F99 K103 I104 E105 E111 T124 T147 E F158 S159 M163 F197 T5 Q6 I29 N31 Y32 N50 S63 Y87 Q89 K107 R Score per residue for model 26 Q32 G33 Q34 E37 K97 R98 F99 I104 E T124 S125 M F146 T147 M148 S152 E135 L M163 P F197 L232 S10 L11 V19 I29 Y32 L46 D56 L78 N85 Y86 Y87 F91 G101
17 Page 17 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 27 R4 2 G22 E25 V47 E51 S52 N53 K93 E105 Y121 L M163 S164 P170 G171 Y224 A226 R227 S26 W35 L46 L47 V58 P59 S67 G68 T72 P80 Y86 Y87 W92 G101 K107 R Score per residue for model 28 2 M20 D35 V40 F46 K55 C71 V72 L73 N107 F117 Y121 I122 T124 T147 S154 G183 G K194 N213 4 S26 W35 N50 T53 L54 S63 S67 G68 W92 3 K107 R Score per residue for model 29 2 G22 E25 L31 D35 M36 Q48 I56 K74 D75 K103 P118 W120 Y S152
18 Page 18 Full wwpdb NMR Structure Validation Report 2KH G183 P N213 4 A226 K231 L232 S7 7 T20 T72 L73 Y86 G101 S129 S Score per residue for model 30 R4 2 G22 E25 K103 I104 Y121 T F146 T147 F150 V151 S152 S129 P F158 S M163 P170 L208 S248 H249 I2 S10 L11 S26 W35 K39 L46 L47 N50 T53 L54 S67 G68 P80 A84 W Score per residue for model L31 Q32 M36 V41 K55 S70 C71 L80 Q81 S84 V85 F99 K103 I104 Q116 W120 Y121 T124 E128 K138
19 Page 19 Full wwpdb NMR Structure Validation Report 2KH2 L F158 S159 M163 Y224 R227 S248 M4 T20 R24 N31 Y32 L46 A51 R61 G68 S77 Q89 F91 F98 G Score per residue for model 32 M20 Q32 V40 K55 C71 V72 L73 F117 Y121 I F158 S M163 S P170 A221 T5 T20 I29 Q37 Q38 L46 L47 D56 A84 W92 3 Q100 K107 R Score per residue for model 33 R4 2 Q14 Q15 L31 Q32 M36 N53 D54 K55 C71 S84 V85 N89 K103 I104 E105 N107 Q116 F150 V151 S152 G241 6 P F K194 D202 Y209 Y223 Y224 A226 R227 K231 T20 W35 Y36 D56 T72 S76 W92 3 K103
20 Page 20 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 34 S5 Q14 Q15 K16 M44 E50 S70 S84 V85 F99 T124 S125 M F146 T147 M F197 K231 T5 S26 I29 N31 Y32 Q38 L46 K52 T53 L54 G64 S65 T72 A84 R Score per residue for model 35 A28 L29 D35 M36 E37 V47 K55 S84 V85 N89 K93 K94 K103 I104 W120 Y G239 L F158 S159 S164 W165 V166 R167 P K194 F197 M4 S26 Q38 T72 L73 A84 N85 F98 G99 R Score per residue for model 36 N7 C8 T9 2 S17 L31 D35 M36 C71 L80 Q81 K93 F99 K103 I104 E113 Y121 I M130 S152
21 Page 21 Full wwpdb NMR Structure Validation Report 2KH2 S248 H249 L S154 F197 R216 A217 E218 D219 K231 Y237 W238 T5 S10 L11 S26 P44 N50 D56 S67 G68 S Score per residue for model 37 2 C71 V72 L73 S84 V85 K97 15 Q116 F117 P118 T124 S152 K231 S129 V166 R P170 P K194 V222 M4 S10 L11 S12 3 S26 I29 N31 Y32 Q37 L46 L47 N50 T53 L54 S67 G68 T72 L78 Q89 F98 G Score per residue for model 38 R4 Q34 F46 E51 S52 N53 C71 N89 K93
22 Page 22 Full wwpdb NMR Structure Validation Report 2KH2 S M163 F197 D202 N203 S248 H249 M4 7 I29 N31 Y32 P80 F91 W Score per residue for model 39 Q48 C71 N89 E113 W120 Y121 I122 T124 S M148 S152 6 L F158 S159 G183 G184 F197 L208 R227 K231 S T22 S26 Q37 Q38 K39 K42 L47 N50 A51 I75 S76 K107 R Score per residue for model 40 C8 A28 L29 Q32 E50 N53 L73 F99 E105 N107 F S248 E135 6 P M163 L208 Y209 T5 L11 T20 I21 S26 I29 L46 L47 N50 L54 R61 F62 T72 L73 S76 Q89 F91 W92 3
23 Page 23 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 41 S5 M20 A28 L29 D35 V40 V41 V47 L73 S84 V85 K93 K94 E113 H F158 S P K194 L232 S7 P8 T22 S26 Q38 P44 L46 D56 F Score per residue for model 42 R4 S5 L29 Q32 M44 N53 D54 K55 K74 D75 K97 K103 I104 N107 E F150 V151 S152 P F158 S159 M163 V166 F197 L208 Y209 S248 H249 H250 T20 I21 T22 S26 Q38 N50 L54 G64 S65 S67 G68 I75 S76 N85 Q89 F91 W Score per residue for model 43
24 Page 24 Full wwpdb NMR Structure Validation Report 2KH2 R4 T9 2 S17 F46 S52 F99 45 F150 V151 S152 Y237 G241 S248 H249 Q Y223 Y224 T5 S12 G16 T20 W35 K52 S65 S77 P80 Y86 Y87 G101 K107 R Score per residue for model 44 R4 2 L29 S45 F46 N53 L73 N107 F117 P S152 S129 L M163 S164 D202 Y209 N213 4 T5 G16 T22 I29 N31 Y32 W35 K39 K42 N50 S63 I75 S76 S77 Y86 Y87 Q89 F91 W92 G Score per residue for model 45 P2 S5 N7 C8 2 A28 L29 F99 E105 E113 T124 S125 P131 T147 M148 F150
25 Page 25 Full wwpdb NMR Structure Validation Report 2KH V177 S10 L11 V19 T20 I21 T22 C23 R24 N31 Y32 W35 Y36 Q37 Q38 L46 L47 N50 R61 T72 I75 S76 A84 Q89 F Score per residue for model 46 2 D35 S45 N53 D54 K55 I56 C71 K97 R98 F99 N D202 Y209 N213 4 Y223 Y224 K231 G241 T5 Q6 S7 P8 Q38 K39 K42 K52 S65 A84 Q89 W Score per residue for model 47 C8 2 Q32 G33 C71 S84 V85 F99 K103 I104 E105 E111 Q T147 M148 S152 S10 L11 7 T20 I29 N31 Y32 W35 6
26 Page 26 Full wwpdb NMR Structure Validation Report 2KH2 S P170 G183 G K194 S Score per residue for model 48 2 S45 F46 V47 D54 N89 K93 K94 E113 W120 Y121 I122 Q V166 R167 P K194 F197 A226 S248 H249 H250 S10 L11 S12 3 V19 T20 W35 T72 Y87 Q89 F98 K107 R Score per residue for model R4 S5 2 Q14 Q15 K16 L29 Q32 F46 E50 D54 K55 I56 L73 S84 V85 F99 K103 I104 E113 F117 Y121 I122 H250 S F158 S P N206 4 K231 L232 I2 3 T20 I21 T22 S26 W35 N50 T53 S76 P80 Q89 F91 W92
27 Page 27 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 50 S5 N7 C8 2 S43 F46 L80 Q81 L82 E83 F99 E105 T147 S152 S V166 R167 G183 Y223 Y224 A226 R227 Y237 W238 G241 T5 S10 L11 S26 P44 K52 S63 Q89 F91 W92 3 K107 R Score per residue for model 51 2 M44 E50 A59 K93 K94 I104 N107 E111 L133 P S F197 Y224 Y237 W238 S12 3 T20 W35 P44 L46 L47 N50 S67 G68 W92 E105 K107 R Score per residue for model 52 R4 S5 2 K16 D35 M36 E37 M44 N53 L73 E105 N107 F117 Y121 S F146 T147 F150 V151 S152
28 Page 28 Full wwpdb NMR Structure Validation Report 2KH2 Y224 Y237 Q132 P V F197 D202 N206 Y209 M4 L11 T22 I29 N31 Y32 Q38 K39 K42 N50 S77 A84 W92 3 F98 G99 R Score per residue for model 53 2 S17 L31 D35 M36 V47 I56 S84 V85 K93 K94 K103 I104 E105 N107 E111 K138 S S K231 S248 H249 S26 I29 Y32 S129 L Score per residue for model 54 R4 S5 T9 L10 R11 2 M20 L26 L31 M36 I56 2 L82 E83 S84 V85 K M148
29 Page 29 Full wwpdb NMR Structure Validation Report 2KH2 L133 S N213 4 A226 S248 H249 H250 T5 S26 N31 Y32 Q38 A84 N85 Y86 W92 3 G Score per residue for model 55 P2 V3 R4 S5 2 M20 L26 A28 Q32 D35 V40 S70 C71 F99 E105 T124 K F150 6 S M163 P K194 Y209 I21 T22 C23 R24 N28 I29 N31 Y32 Q38 K39 K42 N50 A51 T72 L73 S76 A84 Q89 F91 W Score per residue for model 56 R4 2 Q48 C71 S84 P131 K F146 T147 M148 S152 S248 H249 6 S154 S M163 F197 N213 4 S7 P8 S10 L11 7 R18 V19 I29 N31 Y32 L46 K52 D56 S65 T72 W92 3
30 Page 30 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 57 2 L31 M36 F99 E105 T M130 A226 R227 P143 S F158 S V S10 L11 V19 T22 Q37 Q38 L46 L47 N50 A51 K52 D56 R61 G64 S65 T72 I75 S76 P80 A84 Q Score per residue for model 58 T9 2 L31 D35 M36 V47 D54 C71 N89 K93 K97 R98 F99 K103 I104 E W120 Y121 T124 F150 P T22 C23 R24 S26 I29 N31 Y32 K39 A84 N85 F Score per residue for model 59
31 Page 31 Full wwpdb NMR Structure Validation Report 2KH2 P2 V3 R4 2 G22 E25 S84 V85 N89 F99 N107 T147 M148 L S F197 Y224 L243 V244 T5 L11 S26 W35 N50 D56 S77 W Score per residue for model 60 2 L31 M36 E37 K55 I56 S84 V85 N89 K93 K103 N107 W120 Y121 I122 K S Y209 N213 4 Y224 T5 7 K39 S67 S76 Q100 L Score per residue for model 61 K55 C71 Y121
32 Page 32 Full wwpdb NMR Structure Validation Report 2KH2 E130 V131 Q F158 S K194 A226 Y237 7 W35 K52 S63 P80 Q89 F91 S Score per residue for model 62 L29 D35 K C71 V72 L73 S84 V85 K103 I104 Q116 F117 P118 T124 S125 Q F146 T147 M148 H250 L133 V134 E S154 S M163 P190 F197 N213 4 S12 G16 V19 L46 L47 T53 L54 G64 S65 I75 S76 S77 F98 E105 K107 R Score per residue for model T147 N7 M20 Y24 L29 Q32 V41 F42 S43 P57 V58 A C71 V72 L73 S84 V85 K97 N Q116 F F M163 N206 N213 4 A226 R227 Q240 G241 H251 T5 Q6 T20 V58 S65 S67 G68 F98 G99 Q100 E135
33 Page 33 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 64 2 E50 K55 I56 P57 K65 C71 F99 T124 P131 T147 M148 S152 S129 S P F197 Q38 N50 T72 S76 P80 A84 Q Score per residue for model 65 T9 2 Q32 F99 45 S P K194 N213 4 Y223 Y224 A226 R227 G241 T5 S10 L11 T20 N50 T72 L73 I75 S76 F Score per residue for model 66
34 Page 34 Full wwpdb NMR Structure Validation Report 2KH2 2 K16 Q32 G33 Q34 E50 D54 C71 K103 I104 E105 N107 Q116 F117 P118 T124 S152 W238 P F158 S V166 R167 P K231 L232 Y237 I2 T5 Q6 S7 S T22 N31 Y32 L46 L47 A51 D56 G64 S65 S76 F91 F98 E Score per residue for model 67 M36 S45 F46 V47 K55 K93 F150 V151 S152 E135 P K194 F197 M4 S12 T22 I29 Q38 K52 G64 S65 A84 Q89 F91 W92 3 E Score per residue for model 68 P2 V3 R4 S5 N7 C8 T9 2 A28 L29 Q32 S43 M44 S45 I56 C71 D75 F99 K103 N107 T124 P131 T147
35 Page 35 Full wwpdb NMR Structure Validation Report 2KH2 G241 L133 V134 E135 G138 C S P K194 F197 L208 Y209 T5 Q6 S7 R18 T22 L46 L47 K52 T53 L54 G64 S65 I75 Q89 F91 W Score per residue for model 69 L31 M36 V47 L73 F99 E105 F117 T124 S125 M130 F150 V151 S152 A226 R227 S129 6 S F158 S M163 P F197 7 R18 V19 S26 K52 T53 S65 L78 Q89 F91 R Score per residue for model 70 T9 2 L18 L26 A28 Q32 M36 Q39 E51 S52 N53 I56 2 S84 V85 E105 S125 P131 S152 V131 6 S F158 S R P170 D219 Y237 S248 T5 L11 T20 I29 N31 Y32 Q38 K39 K42 T53 G68 A84 K107 R108
36 Page 36 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 71 R4 2 D35 S45 F46 V47 Q48 E51 K55 I56 P57 V58 K93 K94 N107 E113 K231 L232 S129 L P K194 F197 3 T20 S26 W35 Q38 K52 S63 G64 S65 L78 A84 N85 Q Score per residue for model F146 T147 S152 2 Q14 Q15 K16 S17 L18 V19 M20 L26 L31 M36 S45 F46 V47 S52 N53 I56 S84 V100 F101 E113 Y121 I122 T124 S125 K205 N206 A226 K231 T5 Q6 S7 P8 S10 L11 V19 P80
37 Page 37 Full wwpdb NMR Structure Validation Report 2KH Score per residue for model 73 R4 2 Q32 F46 E105 T147 6 L F P K194 A226 R227 S W35 Q38 L46 L47 N50 A51 K52 T53 V58 P59 S76 A84 K Score per residue for model 74 T9 D35 V41 N53 D54 K55 K103 I104 E105 N107 T124 T147 F150 K231 L232 S129 E F158 S159 S164 G183 G184 N206 T5 L11 7 R18 V19 T22 S26 W35 Q38 N50 A51 K52 D56 R61 S65 I75 A84 Q89 F91 R Score per residue for model 75
38 Page 38 Full wwpdb NMR Structure Validation Report 2KH2 R4 S5 N7 C8 2 L31 M36 F46 E50 N53 I56 D75 K103 Y121 I122 T124 T147 F150 P K194 F197 L208 Y209 W92 3 S129 E130 V131 Q132 L133 V134 E S154 G155 F M P170 Q6 S10 L11 V19 T20 C23 R24 N31 Y32 W35 Y36 Q37 Q38 L46 L47 K52 R61 S65 I75 S76 S77 L78 N85 Q89 F Score per residue for model 76 T9 2 L29 Q32 V47 C71 K74 E105 T F146 T147 H250 L140 S F197 M4 T20 Q38 A51 K52 T53 S77 A84 F91 F98 G Score per residue for model 77 S17 E25 L29 M44 S52 N53 D54 K65 N66 V85 N89 E105 T124 E128
39 Page 39 Full wwpdb NMR Structure Validation Report 2KH2 62 V F197 K231 S12 Q38 L46 D56 I75 S76 A84 Y87 E F158 S159
40 Page 40 Full wwpdb NMR Structure Validation Report 2KH2 5 Refinement protocol and experimental data overview i simulated annealing, molecular dynam- The models were refined using the following method: ics. Of the 77 calculated structures, 77 were deposited, based on the following criterion: all calculated structures submitted. The following table shows the software used for structure solution, optimisation and refinement. Software name Classification Version Haddock structure solution 2.0 Haddock refinement 2.0 No chemical shift data was provided. No validations of the models with respect to experimental NMR restraints is performed at this time.
41 Page 41 Full wwpdb NMR Structure Validation Report 2KH2 6 Model quality i 6.1 Standard geometry i There are no covalent bond-length or bond-angle outliers. Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying if the center is modelled as a planar moiety or with the opposite hand. A planarity outlier is detected by checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of a sidechain that are expected to be planar. Mol Chain Chirality Planarity 1 A 0.1± ±0.0 2 B 0.0± ±0.0 All All 8 0 There are no bond-length outliers. There are no bond-angle outliers. All unique chiral outliers are listed below. They are sorted by the frequency of occurrence in the ensemble. Mol Chain Res Type Atoms Models (Total) 2 B 76 SER CA 1 1 A 58 VAL CA 1 1 A 59 ALA CA 1 1 A 1 ALA CA 1 1 A 4 ARG CA 1 1 A 6 LEU CA 1 1 A 7 ASN CA 1 2 B 205 LYS CA 1 There are no planarity outliers. 6.2 Too-close contacts i In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms and hydrogen atoms in each chain respectively. The H(added) column lists the number of hydrogen atoms added and optimized by MolProbity. The Clashes column lists the number of clashes averaged over the ensemble. Mol Chain Non-H H(model) H(added) Clashes 1 A ±3 2 B ±5 Continued on next page...
42 Page 42 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Mol Chain Non-H H(model) H(added) Clashes All All The all-atom clashscore is defined as the number of clashes found per 1000 atoms (including hydrogen atoms). The all-atom clashscore for this structure is 4. All unique clashes are listed below, sorted by their clash magnitude. Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 2:B:94:LEU:HG 2:B:95:PRO:HA :A:12:ASP:HB2 1:A:143:ILE:HG :A:108:ASN:HB3 2:B:185:GLY:HA :B:142:GLN:HG2 2:B:248:SER:HA :B:168:GLN:HB2 2:B:174:LEU:HG :B:180:ILE:HB 2:B:199:ILE:HG :B:212:MET:HB3 2:B:215:LEU:HD :A:104:ILE:HB 1:A:111:GLU:HG :B:49:TYR:HE1 2:B:55:ALA:HA :B:180:ILE:HB 2:B:199:ILE:H :A:63:LYS:HG2 1:A:64:GLU:HG :A:109:LYS:HE3 1:A:147:THR:HG :B:202:ASP:HB2 2:B:209:TYR:HE :B:52:LYS:HG2 2:B:65:SER:HA :B:157:ASP:HB2 2:B:160:ARG:HB :B:4:MET:HB2 2:B:99:GLY:HA :B:227:ARG:HB3 2:B:227:ARG:HH :A:102:ASN:HB2 1:A:113:GLU:HB :B:230:LYS:HG3 2:B:231:LYS:H :A:4:ARG:HB2 1:A:46:PHE:HD :B:189:PHE:HZ 2:B:197:PHE:HB :B:46:LEU:HD22 2:B:236:ASP:HA :B:30:HIS:HA 2:B:68:GLY:HA :B:91:PHE:HB2 2:B:233:THR:HG :A:44:MET:HB2 1:A:58:VAL:HB :A:109:LYS:HB3 1:A:145:ASP:HB :B:48:ILE:HG21 2:B:64:GLY:HA :B:34:THR:O 2:B:88:CYS:HA :B:165:TRP:HB2 2:B:178:ALA:HB :A:31:LEU:HG 1:A:36:MET:HA :B:33:LEU:H1 2:B:88:CYS:HB :B:39:LYS:HB2 2:B:42:LYS:HB :A:150:PHE:HB3 2:B:94:LEU:H :B:66:GLY:HA3 2:B:71:PHE:HA Continued on next page...
43 Page 43 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 2:B:180:ILE:H1 2:B:201:ARG:HB :B:157:ASP:HB3 2:B:160:ARG:HB :A:150:PHE:HB3 2:B:94:LEU:HD :A:105:GLU:HA 1:A:110:LEU:HA :B:29:ILE:HB 2:B:32:TYR:HB :B:168:GLN:HB2 2:B:174:LEU:HD :B:33:LEU:H1 2:B:88:CYS:HB :A:4:ARG:HB2 2:B:92:TRP:HZ :A:86:ASP:OD2 1:A:88:LYS:HG :B:229:ASN:HD22 2:B:236:ASP:HB :B:163:MET:HG2 2:B:180:ILE:HG :A:54:ASP:HA 2:B:231:LYS:NZ :A:18:LEU:HD23 1:A:28:ALA:HB :B:141:VAL:HG21 2:B:147:LEU:HG :B:49:TYR:HE2 2:B:55:ALA:HA :B:149:LEU:H2 2:B:210:LEU:HD :A:149:GLN:HG3 2:B:188:TYR:H :B:19:VAL:HB 2:B:75:ILE:HB :B:220:THR:HG23 2:B:245:THR:HA :B:176:TRP:HZ2 2:B:179:TYR:HB :B:12:SER:HB3 2:B:107:LYS:HD :B:142:GLN:HA 2:B:247:SER:O :B:44:PRO:HD2 2:B:238:TRP:HB :A:21:SER:HB2 1:A:27:LYS:HG :B:95:PRO:O 2:B:96:PHE:HB :B:94:LEU:CG 2:B:95:PRO:HA :B:198:THR:HB 2:B:211:GLN:HB :B:33:LEU:HB3 2:B:51:ALA:HB :A:54:ASP:HB2 1:A:105:GLU:HB :A:97:LYS:HE3 1:A:115:ALA:HB :B:35:TRP:HB2 2:B:48:ILE:HB :B:191:ASP:HA 2:B:194:LYS:HD :B:162:ASP:O 2:B:181:SER:HA :B:37:GLN:HB2 2:B:47:LEU:H :A:4:ARG:HB2 2:B:92:TRP:CZ :B:170:PRO:HD3 2:B:221:ALA:HA :B:157:ASP:HB3 2:B:160:ARG:HB :B:230:LYS:HB2 2:B:234:TRP:HE :B:230:LYS:HD3 2:B:234:TRP:HZ :A:105:GLU:HG2 1:A:110:LEU:HD :B:178:ALA:HB3 2:B:199:ILE:H Continued on next page...
44 Page 44 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 1:A:110:LEU:HD21 1:A:148:MET:HB :B:39:LYS:HG2 2:B:84:ALA:HB :A:105:GLU:HB3 1:A:110:LEU:HB :A:56:ILE:HB 1:A:103:LYS:HE :B:18:ARG:HH11 2:B:76:SER:HA :B:46:LEU:HD21 2:B:49:TYR:HB :A:4:ARG:HB3 2:B:92:TRP:CH :A:92:LYS:HE3 1:A:95:MET:HA :A:4:ARG:HB3 2:B:92:TRP:CZ :B:80:PRO:HA 2:B:106:ILE:H :B:190:PRO:HG2 2:B:193:VAL:HG :A:149:GLN:HG3 2:B:188:TYR:C :A:97:LYS:HA 1:A:100:VAL:HG :B:34:THR:HB 2:B:89:GLN:HB :B:87:TYR:HB3 2:B:98:PHE:HD :A:96:GLU:HB2 1:A:99:PHE:HD :A:86:ASP:O 1:A:88:LYS:HG :B:176:TRP:CZ2 2:B:179:TYR:HB :B:135:GLU:HG2 2:B:225:CYS:HB :A:108:ASN:HB3 2:B:185:GLY:CA :B:163:MET:HG3 2:B:208:LEU:H :A:147:THR:HB 2:B:186:SER:HA :A:55:LYS:HE2 1:A:102:ASN:HB :A:21:SER:HB2 1:A:27:LYS:HE :B:172:LYS:HG2 2:B:173:ARG:H :A:55:LYS:HG2 1:A:104:ILE:HG :B:46:LEU:H1 2:B:49:TYR:HB :B:140:LEU:H2 2:B:245:THR:HB :B:85:ASN:HB2 2:B:87:TYR:HE :B:202:ASP:HB2 2:B:209:TYR:CE :B:38:GLN:O 2:B:84:ALA:HB :B:193:VAL:HB 2:B:197:PHE:HD :A:74:LYS:HD2 1:A:79:THR:HB :B:11:LEU:H1 2:B:19:VAL:HG :A:8:CYS:HB3 1:A:150:PHE:H :B:98:PHE:HB2 2:B:174:LEU:HB :A:86:ASP:HB3 1:A:89:ASN:HB :B:169:ALA:HB3 2:B:172:LYS:HB :A:6:LEU:HB3 1:A:150:PHE:HE :B:94:LEU:HB3 2:B:95:PRO:HA :B:46:LEU:HB2 2:B:236:ASP:HA Continued on next page...
45 Page 45 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 2:B:157:ASP:CB 2:B:160:ARG:HB :A:126:GLN:HE22 1:A:143:ILE:HG :A:63:LYS:O 1:A:64:GLU:HG :B:1:ASP:HB3 2:B:95:PRO:HD :B:153:ALA:HB1 2:B:156:PHE:CZ :A:6:LEU:H2 1:A:44:MET:HB :A:4:ARG:HB2 2:B:92:TRP:HZ :B:142:GLN:HG2 2:B:143:PRO:HD :B:162:ASP:OD2 2:B:181:SER:HA :A:28:ALA:HB3 1:A:124:THR:HG :B:179:TYR:HB3 2:B:188:TYR:HB :B:94:LEU:HG 2:B:95:PRO:CA :B:141:VAL:O 2:B:246:VAL:HA :A:97:LYS:HE2 1:A:115:ALA:HB :B:52:LYS:HG3 2:B:64:GLY:O :A:46:PHE:HE2 2:B:92:TRP:HE :B:226:ALA:HB1 2:B:235:PHE:C :B:229:ASN:ND2 2:B:236:ASP:HB :B:168:GLN:HB3 2:B:224:TYR:HE :A:125:SER:HB2 1:A:130:MET:HG :B:193:VAL:HB 2:B:197:PHE:C :A:56:ILE:H1 2:B:231:LYS:NZ :A:123:SER:HA 1:A:143:ILE:O :A:138:LYS:HG3 1:A:144:THR:HB :A:105:GLU:HG2 1:A:110:LEU:HB :B:89:GLN:HG2 2:B:90:HIS:N :A:48:GLN:HB3 1:A:94:LYS:HD :B:43:ALA:HB1 2:B:238:TRP:HB :B:182:SER:HA 2:B:201:ARG:CZ :B:142:GLN:HG3 2:B:248:SER:HA :A:105:GLU:HG3 1:A:110:LEU:HB :B:176:TRP:CH2 2:B:179:TYR:HB :A:106:ILE:HG13 1:A:107:ASN:H :A:147:THR:HB 1:A:149:GLN:OE :A:14:GLN:HB3 1:A:16:LYS:HG :A:150:PHE:CE2 2:B:93:SER:HA :A:45:SER:HB2 1:A:59:ALA:HB :A:108:ASN:O 2:B:183:GLY:HA :A:4:ARG:NH1 2:B:30:HIS:HB :A:109:LYS:HE3 1:A:147:THR:HG :B:38:GLN:HB2 2:B:44:PRO:HB Continued on next page...
46 Page 46 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 1:A:138:LYS:HA 1:A:144:THR:HG :B:169:ALA:HB3 2:B:172:LYS:HE :B:80:PRO:HA 2:B:106:ILE:HG :A:9:THR:HG21 1:A:39:GLN:HG :A:41:VAL:HB 1:A:63:LYS:HD :B:14:SER:O 2:B:17:ASP:HB :A:73:LEU:HG 1:A:117:PHE:CZ :A:44:MET:HA 1:A:59:ALA:O :B:151:CYS:HB3 2:B:208:LEU:HB :B:100:GLN:HA 2:B:173:ARG:HD :A:1:ALA:N 1:A:2:PRO:HD :A:14:GLN:HB2 1:A:16:LYS:HD :B:199:ILE:H3 2:B:199:ILE:H :B:133:LEU:HB2 2:B:239:GLY:HA :B:25:THR:HG23 2:B:69:THR:HA :A:107:ASN:O 1:A:108:ASN:HB :B:47:LEU:HA 2:B:58:VAL:HG :A:47:VAL:HA 1:A:93:LYS:O :A:108:ASN:O 2:B:181:SER:HB :A:55:LYS:HE2 1:A:104:ILE:HG :B:193:VAL:HB 2:B:197:PHE:CD :B:94:LEU:CB 2:B:95:PRO:HA :B:89:GLN:HG2 2:B:90:HIS:H :B:191:ASP:HA 2:B:194:LYS:HE :A:22:GLY:H 1:A:25:GLU:HB :B:167:ARG:HH12 2:B:219:ASP:HA :A:70:SER:HB2 1:A:99:PHE:CE :B:33:LEU:C 2:B:88:CYS:HB :A:27:LYS:HA 1:A:131:PRO:HA :A:103:LYS:HD2 1:A:110:LEU:H :B:189:PHE:HE1 2:B:199:ILE:H :A:113:GLU:HB2 1:A:121:TYR:CE :B:132:GLN:HA 2:B:237:TYR:OH :B:227:ARG:HB3 2:B:227:ARG:NH :B:52:LYS:HG2 2:B:64:GLY:O :A:111:GLU:HG2 1:A:145:ASP:HA :A:46:PHE:HA 1:A:58:VAL:HG :A:17:SER:HB2 1:A:31:LEU:HD :B:94:LEU:HD21 2:B:190:PRO:HA :B:12:SER:HA 2:B:105:GLU:O :B:189:PHE:O 2:B:194:LYS:HE Continued on next page...
47 Page 47 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 2:B:176:TRP:HE3 2:B:190:PRO:HG :A:20:MET:HG2 1:A:40:VAL:HG :B:189:PHE:HE2 2:B:199:ILE:H :A:150:PHE:HB3 2:B:94:LEU:H :B:6:GLN:OE1 2:B:99:GLY:HA :B:140:LEU:H1 2:B:247:SER:HB :B:156:PHE:CE2 2:B:227:ARG:HD :B:50:ASN:HA 2:B:91:PHE:HZ :A:21:SER:OG 1:A:27:LYS:HE :A:104:ILE:HB 1:A:111:GLU:HB :A:54:ASP:HA 1:A:105:GLU:HB :B:223:TYR:O 2:B:241:GLY:HA :B:13:ALA:HB3 2:B:78:LEU:HD :A:6:LEU:O 1:A:7:ASN:HB :A:110:LEU:H2 1:A:148:MET:HB :B:135:GLU:CG 2:B:225:CYS:HB :A:6:LEU:HG 1:A:44:MET:HB :B:29:ILE:HG22 2:B:92:TRP:HB :A:123:SER:HB3 1:A:142:ASP:HB :B:16:GLY:HA2 2:B:77:SER:HB :B:39:LYS:HE2 2:B:81:GLU:O :B:1:ASP:HB2 2:B:95:PRO:HD :A:4:ARG:HB2 1:A:46:PHE:HB :B:96:PHE:CE1 2:B:233:THR:HG :B:61:ARG:O 2:B:75:ILE:HA :B:12:SER:HB3 2:B:107:LYS:HD :A:147:THR:HB 2:B:188:TYR:CE :B:142:GLN:HG3 2:B:249:HIS:HD :B:38:GLN:HB3 2:B:85:ASN:O :A:36:MET:HG2 1:A:39:GLN:NE :B:46:LEU:HB2 2:B:235:PHE:O :A:153:SER:H 2:B:94:LEU:H :A:109:LYS:HE3 1:A:147:THR:CG :A:104:ILE:H2 1:A:121:TYR:CE :B:177:VAL:O 2:B:193:VAL:HG :A:4:ARG:HB2 1:A:46:PHE:CD :A:96:GLU:O 1:A:100:VAL:HG :A:6:LEU:H2 1:A:44:MET:HB :B:157:ASP:CB 2:B:160:ARG:HB :A:104:ILE:H2 1:A:121:TYR:HE :B:24:ARG:HG2 2:B:69:THR:O Continued on next page...
48 Page 48 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 1:A:152:SER:HA 2:B:94:LEU:H :A:55:LYS:HD3 1:A:102:ASN:HB :B:29:ILE:HG22 2:B:92:TRP:HB :B:5:THR:HA 2:B:100:GLN:OE :B:176:TRP:CE3 2:B:190:PRO:HG :A:149:GLN:HG3 2:B:188:TYR:CE :B:141:VAL:HG12 2:B:142:GLN:H :B:50:ASN:HB3 2:B:53:THR:HG :B:133:LEU:HD23 2:B:153:ALA:HA :A:105:GLU:HG3 1:A:110:LEU:HD :B:86:TYR:O 2:B:101:GLY:HA :A:106:ILE:H2 1:A:109:LYS:HG :A:106:ILE:HG22 1:A:107:ASN:H :A:55:LYS:HB2 1:A:104:ILE:HG :A:20:MET:HG2 1:A:40:VAL:HG :B:45:GLN:HE22 2:B:237:TYR:H :B:163:MET:HB2 2:B:180:ILE:HG :A:4:ARG:HB3 2:B:92:TRP:HZ :A:4:ARG:HB3 2:B:92:TRP:NE :B:193:VAL:HB 2:B:197:PHE:H :B:228:GLN:HG3 2:B:234:TRP:O :B:227:ARG:O 2:B:235:PHE:HA :B:49:TYR:CE1 2:B:55:ALA:HA :A:62:LEU:HB3 1:A:65:LYS:HD :A:54:ASP:O 1:A:104:ILE:HA :A:35:ASP:HB3 1:A:38:GLN:HE :B:153:ALA:HB1 2:B:156:PHE:CE :B:32:TYR:O 2:B:90:HIS:HA :B:149:LEU:HB2 2:B:210:LEU:HB :A:6:LEU:H3 1:A:150:PHE:HE :A:108:ASN:HB2 2:B:181:SER:HB :A:6:LEU:HD23 2:B:93:SER:OG :B:48:ILE:H3 2:B:54:LEU:HG :A:20:MET:SD 1:A:26:LEU:HG :B:132:GLN:HA 2:B:237:TYR:CE :A:24:TYR:HE1 1:A:67:LEU:HD :A:50:GLU:O 1:A:57:PRO:HD :A:118:PRO:O 1:A:119:ASN:HB :A:109:LYS:HG3 1:A:145:ASP:HB :B:230:LYS:CG 2:B:231:LYS:H :A:55:LYS:HE3 1:A:104:ILE:HG Continued on next page...
49 Page 49 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 2:B:36:TYR:OH 2:B:234:TRP:HB :A:96:GLU:HB2 1:A:99:PHE:CD :B:199:ILE:H 2:B:199:ILE:H :B:182:SER:HA 2:B:201:ARG:NH :A:52:SER:HB2 1:A:55:LYS:HB :B:35:TRP:C 2:B:48:ILE:HB :A:7:ASN:HB3 1:A:41:VAL:CG :B:230:LYS:HD3 2:B:234:TRP:CZ :B:172:LYS:HG3 2:B:173:ARG:N :B:169:ALA:HB3 2:B:172:LYS:HD :B:143:PRO:HD3 2:B:247:SER:O :B:133:LEU:H3 2:B:225:CYS:HB :B:230:LYS:HE3 2:B:234:TRP:HZ :B:46:LEU:CB 2:B:236:ASP:HA :B:21:ILE:H2 2:B:73:LEU:HD :B:177:VAL:HG12 2:B:193:VAL:HG :B:29:ILE:H1 2:B:33:LEU:HD :B:131:VAL:HB 2:B:237:TYR:CZ :B:44:PRO:HD2 2:B:238:TRP:C :A:26:LEU:H2 1:A:82:LEU:HD :B:34:THR:HB 2:B:36:TYR:CE :B:190:PRO:HD2 2:B:193:VAL:HG :A:55:LYS:HA 1:A:103:LYS:O :B:23:CYS:HB2 2:B:35:TRP:CH :A:150:PHE:HE2 2:B:93:SER:HA :A:58:VAL:HG23 1:A:59:ALA:N :A:47:VAL:HG21 1:A:100:VAL:HG :B:85:ASN:HB2 2:B:87:TYR:CE :B:35:TRP:H 2:B:48:ILE:HB :B:131:VAL:HG13 2:B:156:PHE:CD :B:189:PHE:C 2:B:194:LYS:HG :A:93:LYS:HE2 1:A:93:LYS:HA :A:104:ILE:O 1:A:110:LEU:HA :A:108:ASN:ND2 2:B:183:GLY:HA :B:176:TRP:HE1 2:B:235:PHE:HZ :A:127:ALA:HB3 1:A:130:MET:HG :A:26:LEU:H1 1:A:62:LEU:H :B:19:VAL:HG21 2:B:78:LEU:H :A:12:ASP:OD2 1:A:16:LYS:HB :B:180:ILE:HB 2:B:199:ILE:CG :A:93:LYS:HA 1:A:93:LYS:HE Continued on next page...
50 Page 50 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 2:B:162:ASP:HB3 2:B:228:GLN:NE :A:108:ASN:HD21 2:B:183:GLY:HA :B:190:PRO:HD2 2:B:193:VAL:CG :B:135:GLU:HG2 2:B:225:CYS:HB :B:98:PHE:C 2:B:174:LEU:HB :B:6:GLN:HG2 2:B:88:CYS:SG :A:147:THR:HG22 2:B:188:TYR:CE :B:187:THR:HB 2:B:189:PHE:CE :A:63:LYS:C 1:A:64:GLU:HG :A:63:LYS:O 1:A:65:LYS:HG :B:189:PHE:CZ 2:B:197:PHE:HB :B:157:ASP:O 2:B:160:ARG:HD :A:1:ALA:HB3 2:B:28:ASN:HB :B:157:ASP:HB2 2:B:160:ARG:HB :B:150:SER:HA 2:B:208:LEU:O :B:200:SER:HB2 2:B:209:TYR:HB :B:80:PRO:HA 2:B:106:ILE:C :B:61:ARG:HD2 2:B:77:SER:O :B:91:PHE:CE2 2:B:232:LEU:H :B:189:PHE:HZ 2:B:199:ILE:H :A:51:GLU:HA 1:A:57:PRO:HD :B:36:TYR:HE2 2:B:235:PHE:O :B:163:MET:SD 2:B:227:ARG:HG :B:16:GLY:HA2 2:B:77:SER:OG :B:161:TYR:C 2:B:229:ASN:HA :A:108:ASN:O 2:B:185:GLY:HA :B:142:GLN:HG3 2:B:143:PRO:HD :A:110:LEU:HG 1:A:146:PHE:O :B:216:ARG:HB2 2:B:218:GLU:HG :B:37:GLN:HB2 2:B:47:LEU:C :A:62:LEU:HD22 1:A:67:LEU:H :B:189:PHE:CZ 2:B:199:ILE:H :A:150:PHE:H 2:B:188:TYR:H :B:87:TYR:OH 2:B:173:ARG:HA :A:13:SER:HB3 1:A:109:LYS:NZ :B:66:GLY:HA3 2:B:71:PHE:C :A:105:GLU:HG3 1:A:110:LEU:HG :B:12:SER:CB 2:B:107:LYS:HD :B:157:ASP:HB3 2:B:160:ARG:CB :B:20:THR:HG23 2:B:74:THR:HG :B:18:ARG:NH1 2:B:76:SER:HA Continued on next page...
51 Page 51 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 2:B:235:PHE:HB2 2:B:238:TRP:HE :B:91:PHE:HE2 2:B:232:LEU:H :B:135:GLU:HA 2:B:151:CYS:HA :A:57:PRO:O 1:A:58:VAL:CB :B:4:MET:SD 2:B:90:HIS:HD :A:8:CYS:HB3 1:A:150:PHE:C :A:126:GLN:NE2 1:A:143:ILE:HG :B:147:LEU:H3 2:B:244:VAL:HG :B:230:LYS:HD3 2:B:234:TRP:HZ :B:94:LEU:HD21 2:B:190:PRO:HB :B:49:TYR:CE2 2:B:55:ALA:HA :A:20:MET:SD 1:A:62:LEU:HD :B:33:LEU:HD22 2:B:89:GLN:O :B:52:LYS:HE2 2:B:65:SER:HA :B:13:ALA:O 2:B:106:ILE:HA :A:7:ASN:HB3 1:A:41:VAL:HG :A:121:TYR:CE2 1:A:138:LYS:HB :B:140:LEU:HA 2:B:245:THR:O :A:70:SER:HB3 1:A:81:GLN:HG :A:121:TYR:HB2 1:A:144:THR:HG :B:143:PRO:HA 2:B:246:VAL:HG :B:167:ARG:HA 2:B:222:VAL:O :B:135:GLU:HA 2:B:150:SER:O :B:18:ARG:HA 2:B:75:ILE:O :A:109:LYS:HE3 2:B:185:GLY:HA :B:6:GLN:OE1 2:B:87:TYR:HA :B:52:LYS:HE2 2:B:66:GLY:O :A:32:GLN:HG2 1:A:33:GLY:H :A:57:PRO:O 1:A:58:VAL:HB :B:2:ILE:HB 2:B:90:HIS:CE :A:4:ARG:NH2 2:B:30:HIS:HB :B:52:LYS:HB3 2:B:64:GLY:O :A:15:GLN:OE1 1:A:15:GLN:HA :B:87:TYR:CE1 2:B:101:GLY:HA :B:25:THR:CG2 2:B:69:THR:HA :B:2:ILE:H1 2:B:92:TRP:HE :B:66:GLY:CA 2:B:71:PHE:HA :B:130:GLU:O 2:B:155:GLY:HA :A:92:LYS:HG2 1:A:95:MET:SD :B:94:LEU:H2 2:B:94:LEU:H :A:149:GLN:HA 2:B:188:TYR:CE Continued on next page...
52 Page 52 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Atom-1 Atom-2 Clash(Å) Distance(Å) Models Worst Total 2:B:2:ILE:HG22 2:B:26:SER:HB :A:21:SER:HB2 1:A:27:LYS:HG :B:143:PRO:HA 2:B:246:VAL:CG :B:131:VAL:HA 2:B:155:GLY:HA :A:66:ASN:HB2 1:A:85:VAL:O :B:230:LYS:HB3 2:B:231:LYS:H :B:172:LYS:HG2 2:B:173:ARG:N :A:81:GLN:NE2 1:A:83:GLU:HG :B:78:LEU:HD21 2:B:106:ILE:HG :B:38:GLN:HB3 2:B:85:ASN:ND :B:138:GLY:H 2:B:242:THR:HG :B:34:THR:HB 2:B:36:TYR:HE :A:37:GLU:HA 1:A:37:GLU:OE :A:4:ARG:NH1 2:B:30:HIS:HB :B:55:ALA:HB3 2:B:58:VAL:CG :B:228:GLN:HA 2:B:234:TRP:O :B:54:LEU:HD21 2:B:62:PHE:O :B:135:GLU:HB2 2:B:242:THR:OG :B:89:GLN:HB2 2:B:97:THR:O :B:4:MET:SD 2:B:25:THR:HB :A:21:SER:CB 1:A:27:LYS:HE :B:189:PHE:CE1 2:B:199:ILE:H :B:228:GLN:HG2 2:B:234:TRP:O :B:166:VAL:HG12 2:B:176:TRP:HA :A:107:ASN:CG 1:A:108:ASN:H :A:15:GLN:HA 1:A:15:GLN:OE :B:87:TYR:C 2:B:101:GLY:HA :A:106:ILE:HG13 1:A:107:ASN:N :A:108:ASN:HB3 2:B:181:SER:HB Torsion angles i Protein backbone i In the following table, the Percentiles column shows the percent Ramachandran outliers of the chain as a percentile score with respect to all PDB entries followed by that with respect to all NMR entries. The Analysed column shows the number of residues for which the backbone conformation was analysed and the total number of residues. Mol Chain Analysed Favoured Allowed Outliers Percentiles 1 A 151/153 (99%) 142±2 (94±2%) 9±2 (6±2%) 1±1 (1±1%) Continued on next page...
53 Page 53 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Mol Chain Analysed Favoured Allowed Outliers Percentiles 2 B 234/254 (92%) 217±3 (93±1%) 15±3 (6±1%) 2±1 (1±0%) All All 29645/31339 (95%) (93%) 1820 (6%) 202 (1%) All 35 unique Ramachandran outliers are listed below. occurrence in the ensemble. Mol Chain Res Type Models (Total) 2 B 229 ASN 42 2 B 30 HIS 29 2 B 185 GLY 27 1 A 106 ILE 15 1 A 21 SER 11 1 A 47 VAL 10 2 B 160 ARG 9 2 B 170 PRO 8 1 A 107 ASN 8 2 B 184 GLY 6 2 B 186 SER 6 1 A 2 PRO 4 1 A 108 ASN 3 1 A 53 ASN 2 2 B 182 SER 2 1 A 46 PHE 1 2 B 96 PHE 1 2 B 192 THR 1 2 B 31 ASN 1 2 B 28 ASN 1 1 A 85 VAL 1 1 A 114 SER 1 1 A 58 VAL 1 2 B 241 GLY 1 1 A 49 GLY 1 2 B 27 GLY 1 2 B 177 VAL 1 2 B 97 THR 1 1 A 32 GLN 1 1 A 101 PHE 1 1 A 52 SER 1 2 B 230 LYS 1 1 A 6 LEU 1 2 B 52 LYS 1 1 A 4 ARG 1 They are sorted by the frequency of
54 Page 54 Full wwpdb NMR Structure Validation Report 2KH Protein sidechains i In the following table, the Percentiles column shows the percent sidechain outliers of the chain as a percentile score with respect to all PDB entries followed by that with respect to all NMR entries. The Analysed column shows the number of residues for which the sidechain conformation was analysed and the total number of residues. Mol Chain Analysed Rotameric Outliers Percentiles 1 A 140/140 (100%) 128±3 (91±2%) 12±3 (9±2%) B 200/203 (99%) 171±4 (86±2%) 29±4 (14±2%) 7 47 All All 26180/26411 (99%) (88%) 3130 (12%) All 197 unique residues with a non-rotameric sidechain are listed below. They are sorted by the frequency of occurrence in the ensemble. Mol Chain Res Type Models (Total) 2 B 199 ILE 73 2 B 192 THR 73 2 B 97 THR 73 2 B 33 LEU 72 2 B 234 TRP 70 2 B 45 GLN 69 1 A 13 SER 67 2 B 25 THR 67 2 B 69 THR 65 1 A 77 LYS 61 2 B 242 THR 58 2 B 60 SER 55 1 A 102 ASN 54 2 B 187 THR 53 2 B 109 THR 52 2 B 150 SER 52 2 B 225 CYS 50 2 B 34 THR 50 1 A 79 THR 50 2 B 14 SER 48 2 B 236 ASP 47 1 A 110 LEU 44 1 A 137 THR 44 2 B 181 SER 43 2 B 147 LEU 42 1 A 119 ASN 38 2 B 245 THR 37 2 B 162 ASP 37 Continued on next page...
55 Page 55 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Mol Chain Res Type Models (Total) 2 B 74 THR 36 1 A 149 GLN 34 2 B 182 SER 33 1 A 76 ASP 33 2 B 176 TRP 33 2 B 233 THR 32 1 A 6 LEU 32 2 B 81 GLU 32 2 B 9 SER 32 2 B 228 GLN 32 1 A 71 CYS 30 2 B 154 SER 30 1 A 84 SER 30 2 B 5 THR 28 2 B 159 SER 27 2 B 26 SER 26 2 B 20 THR 26 1 A 124 THR 25 2 B 136 SER 25 1 A 152 SER 24 2 B 163 MET 23 2 B 30 HIS 23 2 B 189 PHE 22 1 A 108 ASN 22 2 B 22 THR 22 2 B 186 SER 22 2 B 50 ASN 22 2 B 76 SER 21 1 A 32 GLN 21 1 A 35 ASP 20 1 A 64 GLU 20 2 B 90 HIS 20 1 A 9 THR 19 2 B 17 ASP 19 2 B 230 LYS 18 1 A 144 THR 17 2 B 11 LEU 17 1 A 29 LEU 17 2 B 157 ASP 17 2 B 94 LEU 16 2 B 88 CYS 16 1 A 145 ASP 15 Continued on next page...
56 Page 56 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Mol Chain Res Type Models (Total) 2 B 129 SER 15 2 B 67 SER 14 2 B 72 THR 14 2 B 56 ASP 14 2 B 214 SER 14 1 A 53 ASN 14 2 B 1 ASP 14 1 A 93 LYS 13 2 B 107 LYS 12 1 A 147 THR 12 2 B 198 THR 12 2 B 7 SER 12 1 A 50 GLU 11 2 B 206 ASN 11 1 A 121 TYR 11 2 B 191 ASP 10 2 B 108 ARG 10 2 B 31 ASN 9 2 B 53 THR 9 2 B 246 VAL 9 1 A 45 SER 9 2 B 63 SER 9 2 B 175 GLU 8 2 B 164 SER 8 2 B 52 LYS 8 2 B 142 GLN 8 2 B 250 HIS 8 2 B 77 SER 7 2 B 227 ARG 7 1 A 5 SER 7 1 A 116 GLN 6 2 B 249 HIS 6 1 A 56 ILE 6 2 B 201 ARG 6 1 A 54 ASP 6 2 B 92 TRP 6 1 A 48 GLN 5 1 A 17 SER 5 1 A 34 GLN 5 2 B 93 SER 5 1 A 150 PHE 5 2 B 24 ARG 5 Continued on next page...
57 Page 57 Full wwpdb NMR Structure Validation Report 2KH2 Continued from previous page... Mol Chain Res Type Models (Total) 2 B 146 SER 5 1 A 39 GLN 5 2 B 166 VAL 5 1 A 125 SER 5 1 A 8 CYS 4 1 A 43 SER 4 2 B 89 GLN 4 2 B 148 ARG 4 1 A 51 GLU 4 1 A 109 LYS 4 1 A 75 ASP 4 1 A 52 SER 4 2 B 247 SER 4 1 A 128 GLU 3 2 B 179 TYR 3 2 B 65 SER 3 1 A 37 GLU 3 1 A 73 LEU 3 2 B 132 GLN 3 1 A 105 GLU 3 1 A 89 ASN 3 2 B 248 SER 3 2 B 231 LYS 3 2 B 70 GLN 3 2 B 173 ARG 3 1 A 142 ASP 3 1 A 123 SER 3 1 A 138 LYS 2 1 A 46 PHE 2 2 B 200 SER 2 2 B 235 PHE 2 1 A 153 SER 2 1 A 106 ILE 2 1 A 55 LYS 2 2 B 85 ASN 2 2 B 130 GLU 2 2 B 12 SER 2 1 A 97 LYS 2 2 B 106 ILE 2 1 A 151 VAL 2 2 B 160 ARG 2 1 A 7 ASN 2 Continued on next page...
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