SMTL ID : 3nxg.1 (1 other biounit)

JC polyomavirus VP1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 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: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:D.53, A:S.54, E:H.104 GOL.4: 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.5: 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: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.53, C:S.54, B:H.104 GOL.7: 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.9: 7 residues within 4Å: Chain D: H.104 Chain E: S.45, S.47, S.52, D.53, S.54, P.55 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.45, E:D.53, E:S.54, D:H.104

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

EDO.2: 5 residues within 4Å: Chain A: H.125, F.127, G.197, T.198 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.198 Water bridges: A:G.197, A:G.197 EDO.3: 4 residues within 4Å: Chain A: F.127, F.196, T.217 Ligands: EDO.2 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain C: H.125, F.127, F.196, G.197, T.198 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Water bridges: B:I.211, C:G.197, C:R.259 EDO.8: 5 residues within 4Å: Chain D: H.125, F.127, F.196, G.197, T.198 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.125 Water bridges: D:G.197, D:G.197 EDO.10: 5 residues within 4Å: Chain E: H.125, F.127, F.196, G.197, T.198 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Water bridges: D:I.211, E:G.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neu, U. et al., Structure-function analysis of the human JC polyomavirus establishes the LSTc pentasaccharide as a functional receptor motif. Cell Host Microbe (2010)

Release Date

2010-11-17

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

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