SMTL ID : 4wdy.1

JC Polyomavirus VP1 five-fold pore mutant N221Q

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-pentamer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: S.45, S.47, S.52, D.53, S.54, P.55, M.59 Chain E: H.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.53, A:S.54 Water bridges: A:N.56 GOL.3: 8 residues within 4Å: Chain A: H.104 Chain B: S.45, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.45, B:D.53, B:S.54, A:H.104 GOL.4: 8 residues within 4Å: Chain B: H.104 Chain C: S.45, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.45, C:D.53, C:S.54, B:H.104 GOL.6: 8 residues within 4Å: Chain C: H.104 Chain D: S.45, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.53, D:S.54 Water bridges: D:S.54, D:N.56 GOL.8: 8 residues within 4Å: Chain D: H.104 Chain E: S.45, S.47, S.52, D.53, S.54, P.55, M.59 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.45, E:S.52, E:S.54, D:H.104 Water bridges: E:S.45

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: H.125, F.127, F.196, G.197, T.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.198 EDO.5: 4 residues within 4Å: Chain C: H.125, F.196, G.197, T.198 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:I.211 Hydrogen bonds: C:G.197 EDO.7: 3 residues within 4Å: Chain D: H.125, G.197, T.198 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:I.211, D:G.197 EDO.9: 5 residues within 4Å: Chain E: H.125, F.127, F.196, G.197, T.198 2 PLIP interactions: 2 interactions with chain E Water bridges: E:G.197, E:G.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nelson, C.D. et al., Modulation of a Pore in the Capsid of JC Polyomavirus Reduces Infectivity and Prevents Exposure of the Minor Capsid Proteins. J.Virol. (2015)

Release Date

2015-02-18

Peptides

Major capsid protein VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Major capsid protein VP1