SMTL ID : 4mj0.1

BK Polyomavirus VP1 pentamer in complex with GD3 oligosaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-pentamer

Ligands

1 x BGC- GAL- SIA- SIA: N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-SIA-SIA.1: 10 residues within 4Å: Chain A: L.37, L.42, K.43, N.247, S.249, T.251, Q.253 Chain B: D.49, F.50 Chain E: H.113 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.37, B:F.50 Hydrogen bonds: A:K.43, A:N.247, A:N.247, A:S.249, A:T.251 Water bridges: A:S.248, A:S.249, B:D.49, B:D.49

2 x SIA- SIA: N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA-SIA.2: 10 residues within 4Å: Chain A: H.113 Chain B: L.37, L.42, K.43, N.247, S.249, T.251, Q.253 Chain C: D.49, F.50 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.37, C:F.50 Hydrogen bonds: B:K.43, B:N.247, B:N.247, B:S.249, B:T.251 Water bridges: B:S.249, B:S.249 SIA-SIA.4: 10 residues within 4Å: Chain D: P.33, D.34, L.37, L.42, K.43, N.247, S.249, T.251, Q.253 Chain E: F.50 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:L.37, E:F.50 Hydrogen bonds: D:K.43, D:N.247, D:N.247, D:S.249, D:T.251 Water bridges: D:K.43, D:S.248, D:S.248, D:S.249 Salt bridges: D:K.43

1 x GAL- SIA- SIA: N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose

GAL-SIA-SIA.3: 10 residues within 4Å: Chain B: H.113 Chain C: L.37, L.42, K.43, N.247, S.249, T.251, Q.253 Chain D: D.49, F.50 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.37, D:F.50 Hydrogen bonds: C:K.43, C:N.247, C:N.247, C:S.249, C:T.251 Water bridges: C:S.248, C:S.249

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: H.125, F.196, G.197, T.198, R.259 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.198, A:T.198, A:T.198, A:R.259 Water bridges: A:G.197, A:G.197 GOL.7: 8 residues within 4Å: Chain B: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.194, B:R.194, B:D.221, B:L.228 Water bridges: B:E.191 GOL.8: 5 residues within 4Å: Chain B: H.125, F.127, F.196, G.197, T.198 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.196, B:T.198 Water bridges: B:G.197, B:G.197 GOL.10: 4 residues within 4Å: Chain C: H.125, F.196, G.197, T.198 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.196, C:T.198, C:T.198 Water bridges: C:G.197, C:G.197 GOL.12: 4 residues within 4Å: Chain D: H.125, F.196, G.197, T.198 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.198 Water bridges: D:G.197, D:G.197 GOL.14: 9 residues within 4Å: Chain E: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228, K.230 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.192, E:R.194, E:R.194, E:D.221, E:D.221, E:K.230, E:K.230 GOL.15: 4 residues within 4Å: Chain E: H.125, F.196, G.197, T.198 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.198, E:T.198 Water bridges: E:G.197, E:G.197

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: P.154, K.155, H.168 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: P.154, K.155, D.167, H.168 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain C: P.154, K.155, D.167, H.168 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain D: P.154, K.155, D.167, H.168 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain E: P.154, K.155, D.167, H.168 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neu, U. et al., A Structure-Guided Mutation in the Major Capsid Protein Retargets BK Polyomavirus. Plos Pathog. (2013)

Release Date

2013-11-06

Peptides

VP1 capsid protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

VP1 capsid protein

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