SMTL ID : 4p3h.3 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

6 x 25G: N-[2-benzyl-4-(1H-tetrazol-5-yl)phenyl]-6-(cyclohexylmethyl)pyridine-2-carboxamide(Non-covalent)

25G.1: 20 residues within 4Å: Chain A: I.41, F.73, L.76, A.77, L.80, A.87, I.102, L.103, W.106, L.107, A.136, F.186, P.189, L.190 Chain D: L.44, P.189, L.190, T.192 Ligands: 25G.11, 25G.12 14 PLIP interactions: 4 interactions with chain D, 10 interactions with chain A Hydrophobic interactions: D:P.189, D:L.190, A:I.41, A:F.73, A:L.76, A:I.102, A:W.106, A:W.106, A:L.107, A:F.186, A:F.186, A:P.189 Hydrogen bonds: D:T.192, D:T.192 25G.2: 20 residues within 4Å: Chain B: I.41, F.73, L.76, A.77, L.80, A.87, I.102, L.103, W.106, L.107, A.136, F.186, P.189, L.190 Chain C: L.44, P.189, L.190, T.192 Ligands: 25G.6, 25G.7 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:I.41, B:F.73, B:L.76, B:I.102, B:W.106, B:W.106, B:L.107, B:F.186, B:F.186, B:P.189, C:P.189, C:L.190 Hydrogen bonds: C:T.192, C:T.192 25G.6: 27 residues within 4Å: Chain B: K.15, E.42, L.44, W.106, A.136, L.137 Chain C: I.41, F.73, L.76, A.77, L.80, A.81, S.84, V.86, A.87, L.99, I.102, L.103, W.106, L.107, F.186, S.188, P.189, L.190, E.191 Ligands: 25G.2, 25G.7 20 PLIP interactions: 16 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.73, C:L.76, C:A.77, C:L.80, C:L.80, C:L.80, C:V.86, C:A.87, C:I.102, C:L.103, C:P.189, C:L.190, B:W.106, B:A.136 Water bridges: C:E.191, C:E.191 pi-Stacking: C:W.106, C:W.106 Hydrogen bonds: B:K.15, B:E.42 25G.7: 18 residues within 4Å: Chain B: R.79, L.80, S.84, V.86, A.87, W.106, L.190 Chain C: I.41, L.44, W.106, L.107, A.136, L.137, P.189 Chain D: R.141, G.142 Ligands: 25G.2, 25G.6 22 PLIP interactions: 6 interactions with chain D, 7 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: D:R.141, C:I.41, C:L.44, C:L.107, C:A.136, C:L.137, B:L.80, B:W.106 Hydrogen bonds: D:R.141, D:R.141, B:R.79, B:S.84, B:A.87 Water bridges: D:G.142, D:G.142, C:Q.18, C:Q.18, B:R.79, B:R.79, B:R.79, B:T.83 pi-Cation interactions: D:R.141 25G.11: 27 residues within 4Å: Chain A: K.15, E.42, L.44, W.106, A.136, L.137 Chain D: I.41, F.73, L.76, A.77, L.80, A.81, S.84, V.86, A.87, L.99, I.102, L.103, W.106, L.107, F.186, S.188, P.189, L.190, E.191 Ligands: 25G.1, 25G.12 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:F.73, D:L.76, D:A.77, D:L.80, D:L.80, D:L.80, D:V.86, D:A.87, D:I.102, D:L.103, D:P.189, D:L.190, A:W.106, A:A.136 pi-Stacking: D:W.106, D:W.106 Hydrogen bonds: A:K.15, A:E.42 25G.12: 18 residues within 4Å: Chain A: R.79, L.80, S.84, V.86, A.87, W.106, L.190 Chain C: R.141, G.142 Chain D: I.41, L.44, W.106, L.107, A.136, L.137, P.189 Ligands: 25G.1, 25G.11 22 PLIP interactions: 7 interactions with chain D, 6 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: D:I.41, D:L.44, D:L.107, D:A.136, D:L.137, C:R.141, A:L.80, A:W.106 Water bridges: D:Q.18, D:Q.18, C:G.142, C:G.142, A:R.79, A:R.79, A:R.79, A:T.83 Hydrogen bonds: C:R.141, C:R.141, A:R.79, A:S.84, A:A.87 pi-Cation interactions: C:R.141

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain B: H.85, V.86, A.89 Chain C: P.90, T.105, W.106, P.108, A.136, R.140 Chain D: R.140 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:H.85, C:T.105, D:R.140, D:R.140 GOL.8: 10 residues within 4Å: Chain A: H.85, V.86, A.89 Chain C: R.140 Chain D: P.90, T.105, W.106, P.108, A.136, R.140 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:R.140, C:R.140, D:T.105, A:H.85

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 5 residues within 4Å: Chain C: P.36, W.51, D.180, L.181, S.182 1 PLIP interactions: 1 interactions with chain C pi-Cation interactions: C:W.51 DMS.5: 5 residues within 4Å: Chain C: T.83, S.84, H.85, R.88, A.89 No protein-ligand interaction detected (PLIP) DMS.9: 5 residues within 4Å: Chain D: P.36, W.51, D.180, L.181, S.182 1 PLIP interactions: 1 interactions with chain D pi-Cation interactions: D:W.51 DMS.10: 5 residues within 4Å: Chain D: T.83, S.84, H.85, R.88, A.89 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gable, J.E. et al., Broad-spectrum allosteric inhibition of herpesvirus proteases. Biochemistry (2014)

Release Date

2014-07-23

Peptides

KSHV protease: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

KSHV protease

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