SMTL ID : 3bwr.1

SV40 VP1 pentamer in complex with GM1 oligosaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-pentamer

Ligands

3 x BGC- GAL- NGA- GAL- SIA: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-NGA-GAL-SIA.1: 13 residues within 4Å: Chain A: Q.37, L.40, K.42, S.43, L.44, A.45, Q.59, N.247, S.249, T.251, Q.253 Chain B: F.50 Chain E: N.113 13 PLIP interactions: 9 interactions with chain A, 3 interactions with chain E, 1 interactions with chain B Hydrogen bonds: A:S.43, A:Q.59, E:N.113, A:Q.37, A:S.43, A:N.247, A:N.247, A:S.249 Water bridges: A:A.46, E:N.113, E:N.113, A:K.42, A:K.42, A:T.248, A:S.249 Hydrophobic interactions: A:T.251, A:Q.37, A:L.40, B:F.50 BGC-GAL-NGA-GAL-SIA.2: 13 residues within 4Å: Chain B: N.113 Chain C: Q.37, L.40, K.42, S.43, L.44, A.45, Q.59, N.247, S.249, T.251, Q.253 Chain D: F.50 11 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:Q.59, C:Q.37, C:S.43, C:S.43, C:S.43, C:N.247, C:S.249 Water bridges: B:N.113, B:N.113, C:T.248 Hydrophobic interactions: C:T.251, C:L.40, D:F.50 BGC-GAL-NGA-GAL-SIA.3: 12 residues within 4Å: Chain A: F.50 Chain D: N.113 Chain E: Q.37, K.42, S.43, L.44, A.45, Q.59, N.247, S.249, T.251, Q.253 11 PLIP interactions: 2 interactions with chain D, 8 interactions with chain E, 1 interactions with chain A Water bridges: D:N.113, D:N.113, E:Q.59, E:T.248, E:T.248 Hydrogen bonds: E:Q.59, E:Q.37, E:S.43, E:N.247, E:N.247, E:S.249, E:T.251 Hydrophobic interactions: E:T.251, A:F.50

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

EDO.4: 6 residues within 4Å: Chain A: F.50, A.141 Chain E: L.40, I.119, F.245, K.255 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.255, E:K.255 EDO.5: 3 residues within 4Å: Chain A: H.125, F.196, R.259 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:T.198, A:R.259 Water bridges: A:G.197, A:R.259, E:I.211 EDO.6: 6 residues within 4Å: Chain A: L.40, I.119, F.245, K.255 Chain B: F.50, A.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.255, A:K.255 EDO.7: 6 residues within 4Å: Chain C: L.40, I.119, F.245, K.255 Chain D: F.50, A.141 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.255 EDO.8: 4 residues within 4Å: Chain D: H.125, F.127, F.196, R.259 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.259 Water bridges: D:R.259 EDO.9: 4 residues within 4Å: Chain E: H.125, F.127, F.196, R.259 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.259 Water bridges: E:R.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neu, U. et al., Structural basis of GM1 ganglioside recognition by simian virus 40. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-03-04

Peptides

Capsid protein VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Capsid protein VP1

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