SMTL ID : 3nxg.2 (1 other biounit)

JC polyomavirus VP1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-10-mer

Ligands

10 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 GOL.11: 8 residues within 4Å: Chain F: S.45, S.47, S.52, D.53, S.54, P.55, M.59 Chain J: H.104 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain J Hydrogen bonds: F:D.53, F:D.53, F:S.54, J:H.104 GOL.14: 7 residues within 4Å: Chain F: H.104 Chain G: S.45, S.47, S.52, D.53, S.54, P.55 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:D.53, G:D.53, G:S.54, F:H.104 GOL.15: 7 residues within 4Å: Chain G: H.104 Chain H: S.45, S.47, S.52, D.53, S.54, P.55 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:D.53, H:D.53, H:S.54, G:H.104 GOL.17: 7 residues within 4Å: Chain H: H.104 Chain I: S.45, S.47, S.52, D.53, S.54, P.55 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:H.104, I:D.53, I:D.53, I:S.54 GOL.19: 7 residues within 4Å: Chain I: H.104 Chain J: S.45, S.47, S.52, D.53, S.54, P.55 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:S.45, J:D.53, J:D.53, J:S.54, I:H.104

10 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: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:G.197, C:R.259, B:I.211 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 E, 1 interactions with chain D Water bridges: E:G.197, D:I.211 EDO.12: 5 residues within 4Å: Chain F: H.125, F.127, G.197, T.198 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain F Water bridges: F:G.197, F:G.197 EDO.13: 4 residues within 4Å: Chain F: F.127, F.196, T.217 Ligands: EDO.12 No protein-ligand interaction detected (PLIP) EDO.16: 5 residues within 4Å: Chain H: H.125, F.127, F.196, G.197, T.198 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:T.198 Water bridges: H:H.125, H:G.197, H:R.259, G:I.211 EDO.18: 5 residues within 4Å: Chain I: H.125, F.127, F.196, G.197, T.198 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:H.125, I:T.198 Water bridges: I:G.197, I:G.197 EDO.20: 5 residues within 4Å: Chain J: H.125, F.127, F.196, G.197, T.198 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:T.198 Water bridges: J:G.197, I:I.211

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: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

Major capsid protein VP1

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