SMTL ID : 1vps.1 (1 other biounit)

POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-pentamer

Ligands

5 x NAG- GAL- SIA- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA-SIA.1: 15 residues within 4Å: Chain A: Y.41, R.46, G.47, N.49, L.50, T.52, S.58, G.60, N.62, T.63, K.155, T.260, N.262, H.267 Chain B: D.54 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.62, A:N.49, A:L.50 Water bridges: A:I.48, A:L.50, A:S.58, A:K.155, A:K.155, A:K.155 Salt bridges: A:K.155 NAG-GAL-SIA-SIA.2: 15 residues within 4Å: Chain B: Y.41, R.46, G.47, N.49, L.50, T.52, E.56, S.58, N.62, T.63, K.155, T.260, N.262, H.267 Chain C: D.54 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.47, B:N.62, B:N.49, B:L.50 Water bridges: B:E.56, B:S.58, B:S.58, B:K.155, B:K.155, B:K.155, B:K.155 Salt bridges: B:K.155 NAG-GAL-SIA-SIA.3: 14 residues within 4Å: Chain C: Y.41, R.46, G.47, N.49, L.50, T.52, S.58, N.62, T.63, K.155, T.260, N.262, H.267 Chain D: D.54 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.47, C:N.62, C:N.49, C:L.50 Water bridges: C:S.58, C:K.155, C:K.155, C:K.155, C:K.155 Salt bridges: C:K.155 NAG-GAL-SIA-SIA.4: 16 residues within 4Å: Chain D: Y.41, R.46, G.47, N.49, L.50, T.52, E.56, S.58, N.62, T.63, K.155, T.260, N.262, V.265, H.267 Chain E: D.54 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.62, D:N.49, D:L.50 Water bridges: D:I.48, D:N.49, D:K.155, D:K.155 Salt bridges: D:K.155 NAG-GAL-SIA-SIA.5: 14 residues within 4Å: Chain A: D.54 Chain E: Y.41, R.46, G.47, N.49, L.50, T.52, S.58, N.62, T.63, T.260, N.262, V.265, H.267 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.62, E:N.49, E:L.50 Water bridges: E:S.58, E:S.58, E:K.155, E:K.155 Salt bridges: E:K.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stehle, T. et al., High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding. Embo J. (1997)

Release Date

1997-05-15

Peptides

POLYOMAVIRUS VP1 PENTAMER: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

POLYOMAVIRUS VP1 PENTAMER

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