SMTL ID : 5e0i.1 (1 other biounit)

Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-hexamer

Ligands

6 x 5J6: methyl 4-(2-bromo-4-fluorophenyl)-6-(morpholin-4-ylmethyl)-2-(1,3-thiazol-2-yl)pyrimidine-5-carboxylate(Non-covalent)

5J6.1: 14 residues within 4Å: Chain A: F.24, P.26, D.30, L.31, T.34, L.38, W.103, I.106, S.107, T.110, F.111, Y.119, I.140, L.141 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.26, A:L.31, A:T.34 Water bridges: A:L.141, A:L.141 Halogen bonds: A:D.30 5J6.2: 20 residues within 4Å: Chain B: F.24, P.26, D.30, L.31, T.34, L.38, W.103, I.106, S.107, T.110, F.111, Y.119, I.140, L.141 Chain C: V.125, W.126, R.128, T.129, A.133, P.135 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:R.128, B:P.26, B:L.31, B:T.34, B:L.141 Hydrogen bonds: C:T.129 Water bridges: B:L.141, B:L.141 Halogen bonds: B:D.30 5J6.3: 14 residues within 4Å: Chain C: F.24, P.26, D.30, L.31, T.34, L.38, W.103, I.106, S.107, T.110, F.111, Y.119, I.140, L.141 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:P.26, C:L.31, C:T.34 Water bridges: C:L.141, C:L.141 Halogen bonds: C:D.30 5J6.4: 20 residues within 4Å: Chain D: F.24, P.26, D.30, L.31, T.34, L.38, W.103, I.106, S.107, T.110, F.111, Y.119, I.140, L.141 Chain E: V.125, W.126, R.128, T.129, A.133, P.135 10 PLIP interactions: 3 interactions with chain E, 7 interactions with chain D Hydrophobic interactions: E:R.128, D:P.26, D:L.31, D:T.34, D:L.141 Hydrogen bonds: E:T.129 Water bridges: E:W.126, D:L.141, D:L.141 Halogen bonds: D:D.30 5J6.5: 14 residues within 4Å: Chain E: F.24, P.26, D.30, L.31, T.34, L.38, W.103, I.106, S.107, T.110, F.111, Y.119, I.140, L.141 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.31, E:T.34 Water bridges: E:L.141, E:L.141 Halogen bonds: E:D.30 5J6.6: 20 residues within 4Å: Chain A: V.125, W.126, R.128, T.129, A.133, P.135 Chain F: F.24, P.26, D.30, L.31, T.34, L.38, W.103, I.106, S.107, T.110, F.111, Y.119, I.140, L.141 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:P.26, F:L.31, F:T.34, A:V.125 Water bridges: F:L.141, F:L.141 Halogen bonds: F:D.30 Hydrogen bonds: A:T.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klumpp, K. et al., High-resolution crystal structure of a hepatitis B virus replication inhibitor bound to the viral core protein. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-12-09

Peptides

Capsid protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Capsid protein

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