SMTL ID : 4wdz.1

JC Polyomavirus VP1 five-fold pore mutant N221W

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-pentamer

Ligands

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: S.123, H.125, T.198, T.200, P.206, P.207, V.208, L.209 Ligands: GOL.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.206, A:V.208, A:V.208 Water bridges: A:S.123, A:S.123, A:T.200 GOL.2: 7 residues within 4Å: Chain A: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.210, A:R.259 Water bridges: A:H.210, A:R.259 GOL.3: 9 residues within 4Å: Chain A: G.121, T.122, G.202, E.203, M.244 Chain E: V.103, T.110, G.116, P.118 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:T.122, A:T.122, A:G.202, E:G.116 Water bridges: A:Q.252, A:Q.252 GOL.4: 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.6: 9 residues within 4Å: Chain A: V.103, T.110, G.116, P.118 Chain B: G.121, T.122, G.202, E.203, M.244 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.116, B:T.122, B:T.122, B:G.202 Water bridges: B:Q.252, B:Q.252 GOL.7: 7 residues within 4Å: Chain A: H.104 Chain B: S.45, S.47, S.52, D.53, S.54, P.55 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.53, B:S.54, A:H.104 GOL.10: 7 residues within 4Å: Chain B: H.104 Chain C: S.45, S.47, S.52, D.53, S.54, P.55 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:H.104, C:D.53, C:S.54 GOL.11: 10 residues within 4Å: Chain B: V.103, T.110, G.116, P.118 Chain C: Q.120, G.121, T.122, G.202, E.203, M.244 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.122, C:T.122, C:T.122, C:Q.252, B:G.116 Water bridges: C:Q.252 GOL.14: 7 residues within 4Å: Chain C: H.104 Chain D: S.45, S.47, S.52, D.53, S.54, P.55 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.53, D:S.54, C:H.104 GOL.15: 10 residues within 4Å: Chain D: V.103, T.110, G.116, P.118 Chain E: G.121, T.122, G.202, E.203, M.244, Q.252 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:T.122, E:T.122, E:T.122, E:Q.252, D:G.116 Water bridges: E:Q.252 GOL.16: 9 residues within 4Å: Chain C: V.103, T.110, G.116, P.118 Chain D: G.121, T.122, G.202, E.203, M.244 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.122, D:T.122, D:T.122, D:Q.252, C:G.116 GOL.17: 7 residues within 4Å: Chain D: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.18 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.210, D:R.259 Water bridges: D:R.259, D:R.259 GOL.19: 7 residues within 4Å: Chain E: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.21 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:V.208, E:H.210, E:R.259, E:R.259 Water bridges: E:V.94 GOL.20: 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:D.53, E:S.54, D:H.104 Water bridges: E:S.45, E:N.56

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

EDO.5: 5 residues within 4Å: Chain A: E.21, K.91, K.262, Q.264 Chain B: E.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.21, A:K.91, A:K.262 EDO.8: 5 residues within 4Å: Chain B: H.125, V.208, L.209, H.210, R.259 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.208, B:H.210, B:R.259 EDO.9: 5 residues within 4Å: Chain B: H.125, F.127, F.196, G.197, T.198 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.197, B:G.197 EDO.12: 7 residues within 4Å: Chain C: E.191, N.192, R.194, D.221, G.226, P.227, L.228 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.192, C:D.221, C:L.228 EDO.13: 4 residues within 4Å: Chain C: H.125, F.196, G.197, T.198 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.197 Water bridges: C:G.197 EDO.18: 5 residues within 4Å: Chain D: H.125, F.196, G.197, T.198 Ligands: GOL.17 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.125 Water bridges: D:G.197, D:G.197 EDO.21: 6 residues within 4Å: Chain E: H.125, F.127, F.196, G.197, T.198 Ligands: GOL.19 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.125 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