SMTL ID : 3njq.2 (2 other biounits)

Crystal structure of Kaposi's sarcoma-associated herpesvirus protease in complex with dimer disruptor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: E.97, L.100, G.148, H.149, W.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.97, A:H.149 Salt bridges: A:H.149 ACT.9: 5 residues within 4Å: Chain C: E.97, L.100, G.148, H.149, W.153 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.97, C:H.149 Salt bridges: C:H.149 ACT.17: 5 residues within 4Å: Chain E: E.97, L.100, G.148, H.149, W.153 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.97, E:H.149 Salt bridges: E:H.149 ACT.25: 5 residues within 4Å: Chain G: E.97, L.100, G.148, H.149, W.153 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:E.97, G:H.149 Salt bridges: G:H.149

12 x NJQ: 3-benzyl-4-({[6-(cyclohexylmethyl)pyridin-2-yl]carbonyl}amino)benzoic acid(Non-covalent)

NJQ.2: 12 residues within 4Å: Chain A: I.41, F.73, L.76, A.77, L.80, I.102, W.106, L.107, A.136, F.186, P.189, L.190 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.41, A:F.73, A:L.76, A:A.77, A:L.80, A:I.102, A:W.106, A:L.107, A:L.107, A:A.136, A:F.186 pi-Stacking: A:W.106 NJQ.7: 13 residues within 4Å: Chain B: L.76, A.77, L.80, V.86, A.87, I.102, L.103, W.106, L.107, S.188, P.189, L.190 Ligands: NJQ.8 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.76, B:A.77, B:L.80, B:L.80, B:V.86, B:A.87, B:I.102, B:L.103, B:W.106, B:L.107, B:P.189, B:L.190 Hydrogen bonds: B:S.188, B:S.188 Water bridges: B:E.191 pi-Stacking: B:W.106, B:W.106 NJQ.8: 9 residues within 4Å: Chain B: I.41, E.42, L.44, W.106, L.107, A.136, L.137 Chain F: R.141 Ligands: NJQ.7 11 PLIP interactions: 3 interactions with chain F, 8 interactions with chain B Hydrophobic interactions: F:R.141, B:I.41, B:E.42, B:L.44, B:W.106, B:L.107, B:A.136, B:L.137, B:L.137 Water bridges: F:G.142 Salt bridges: F:R.141 NJQ.10: 12 residues within 4Å: Chain C: I.41, F.73, L.76, A.77, L.80, I.102, W.106, L.107, A.136, F.186, P.189, L.190 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.41, C:F.73, C:L.76, C:A.77, C:L.80, C:I.102, C:W.106, C:L.107, C:L.107, C:A.136, C:F.186 pi-Stacking: C:W.106 NJQ.15: 13 residues within 4Å: Chain D: L.76, A.77, L.80, V.86, A.87, I.102, L.103, W.106, L.107, S.188, P.189, L.190 Ligands: NJQ.16 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.76, D:A.77, D:L.80, D:L.80, D:V.86, D:A.87, D:I.102, D:L.103, D:W.106, D:L.107, D:P.189, D:L.190 Hydrogen bonds: D:S.188, D:S.188 Water bridges: D:E.191 pi-Stacking: D:W.106, D:W.106 NJQ.16: 9 residues within 4Å: Chain D: I.41, E.42, L.44, W.106, L.107, A.136, L.137 Chain H: R.141 Ligands: NJQ.15 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain H Hydrophobic interactions: D:I.41, D:E.42, D:L.44, D:W.106, D:L.107, D:A.136, D:L.137, D:L.137, H:R.141 Water bridges: H:G.142 Salt bridges: H:R.141 NJQ.18: 12 residues within 4Å: Chain E: I.41, F.73, L.76, A.77, L.80, I.102, W.106, L.107, A.136, F.186, P.189, L.190 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:I.41, E:F.73, E:L.76, E:A.77, E:L.80, E:I.102, E:W.106, E:L.107, E:L.107, E:A.136, E:F.186 pi-Stacking: E:W.106 NJQ.23: 13 residues within 4Å: Chain F: L.76, A.77, L.80, V.86, A.87, I.102, L.103, W.106, L.107, S.188, P.189, L.190 Ligands: NJQ.24 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:L.76, F:A.77, F:L.80, F:L.80, F:V.86, F:A.87, F:I.102, F:L.103, F:W.106, F:L.107, F:P.189, F:L.190 Hydrogen bonds: F:S.188, F:S.188 pi-Stacking: F:W.106, F:W.106 NJQ.24: 9 residues within 4Å: Chain B: R.141 Chain F: I.41, E.42, L.44, W.106, L.107, A.136, L.137 Ligands: NJQ.23 11 PLIP interactions: 8 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:I.41, F:E.42, F:L.44, F:W.106, F:L.107, F:A.136, F:L.137, F:L.137, B:R.141 Water bridges: B:G.142 Salt bridges: B:R.141 NJQ.26: 12 residues within 4Å: Chain G: I.41, F.73, L.76, A.77, L.80, I.102, W.106, L.107, A.136, F.186, P.189, L.190 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:I.41, G:F.73, G:L.76, G:A.77, G:L.80, G:I.102, G:W.106, G:L.107, G:L.107, G:A.136, G:F.186 pi-Stacking: G:W.106 NJQ.31: 13 residues within 4Å: Chain H: L.76, A.77, L.80, V.86, A.87, I.102, L.103, W.106, L.107, S.188, P.189, L.190 Ligands: NJQ.32 16 PLIP interactions: 16 interactions with chain H Hydrophobic interactions: H:L.76, H:A.77, H:L.80, H:L.80, H:V.86, H:A.87, H:I.102, H:L.103, H:W.106, H:L.107, H:P.189, H:L.190 Hydrogen bonds: H:S.188, H:S.188 pi-Stacking: H:W.106, H:W.106 NJQ.32: 9 residues within 4Å: Chain D: R.141 Chain H: I.41, E.42, L.44, W.106, L.107, A.136, L.137 Ligands: NJQ.31 11 PLIP interactions: 3 interactions with chain D, 8 interactions with chain H Hydrophobic interactions: D:R.141, H:I.41, H:E.42, H:L.44, H:W.106, H:L.107, H:A.136, H:L.137, H:L.137 Water bridges: D:G.142 Salt bridges: D:R.141

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain B: H.85, R.88 Chain D: H.85, R.88 Ligands: SO4.11 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Water bridges: B:H.85 Salt bridges: B:H.85, B:R.88, D:H.85, D:R.88 SO4.4: 3 residues within 4Å: Chain B: T.105, W.106 Chain F: R.140 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Water bridges: F:R.140, B:R.140 Salt bridges: F:R.140 Hydrogen bonds: B:T.105 SO4.5: 2 residues within 4Å: Chain B: W.153, R.157 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.153 Salt bridges: B:R.157 SO4.11: 5 residues within 4Å: Chain B: H.85, R.88 Chain D: H.85, R.88 Ligands: SO4.3 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Salt bridges: B:H.85, B:R.88, D:H.85, D:R.88 Water bridges: D:H.85 SO4.12: 3 residues within 4Å: Chain D: T.105, W.106 Chain H: R.140 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain H Hydrogen bonds: D:T.105 Water bridges: D:R.140, H:R.140 Salt bridges: H:R.140 SO4.13: 2 residues within 4Å: Chain D: W.153, R.157 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.153 Salt bridges: D:R.157 SO4.19: 5 residues within 4Å: Chain F: H.85, R.88 Chain H: H.85, R.88 Ligands: SO4.27 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain F Salt bridges: H:H.85, H:R.88, F:H.85, F:R.88 SO4.20: 3 residues within 4Å: Chain B: R.140 Chain F: T.105, W.106 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:T.105 Water bridges: F:R.140, B:R.140 Salt bridges: B:R.140 SO4.21: 2 residues within 4Å: Chain F: W.153, R.157 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:W.153 Salt bridges: F:R.157 SO4.27: 5 residues within 4Å: Chain F: H.85, R.88 Chain H: H.85, R.88 Ligands: SO4.19 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain F Salt bridges: H:H.85, H:R.88, F:H.85, F:R.88 SO4.28: 3 residues within 4Å: Chain D: R.140 Chain H: T.105, W.106 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain D Hydrogen bonds: H:T.105 Water bridges: H:R.140, D:R.140 Salt bridges: D:R.140 SO4.29: 2 residues within 4Å: Chain H: W.153, R.157 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:W.153 Salt bridges: H:R.157

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: P.38, Q.130 Chain B: W.51, D.180, L.181, S.182 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.180, B:S.182, B:S.182 GOL.14: 6 residues within 4Å: Chain C: P.38, Q.130 Chain D: W.51, D.180, L.181, S.182 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.180, D:S.182, D:S.182 GOL.22: 6 residues within 4Å: Chain E: P.38, Q.130 Chain F: W.51, D.180, L.181, S.182 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.180, F:S.182, F:S.182 Water bridges: F:E.35 GOL.30: 6 residues within 4Å: Chain G: P.38, Q.130 Chain H: W.51, D.180, L.181, S.182 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:D.180, H:S.182, H:S.182 Water bridges: H:E.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, G.M. et al., Enzyme inhibition by allosteric capture of an inactive conformation. J.Mol.Biol. (2011)

Release Date

2011-08-17

Peptides

ORF 17: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

ORF 17

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