SMTL ID : 4mj1.1

unliganded BK Polyomavirus VP1 pentamer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-pentamer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: H.125, F.127, F.196, G.197, T.198 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.125, A:T.198, A:T.198 Water bridges: A:G.197, A:G.197, A:R.259, A:R.259 GOL.3: 4 residues within 4Å: Chain B: H.125, F.127, G.197, T.198 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.198 Water bridges: B:G.197, B:G.197, B:R.259, B:R.259, B:R.259 GOL.5: 5 residues within 4Å: Chain C: H.125, F.127, F.196, G.197, T.198 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.198 Water bridges: C:G.197, C:R.259, C:R.259, B:V.211 GOL.7: 5 residues within 4Å: Chain D: H.125, F.127, F.196, G.197, T.198 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.198 Water bridges: D:G.197, D:G.197, D:R.259 GOL.9: 5 residues within 4Å: Chain E: H.125, F.127, F.196, G.197, T.198 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.197, E:T.198 Water bridges: E:G.197, E:R.259, E:R.259

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

CL.2: 4 residues within 4Å: Chain A: P.154, K.155, D.167, H.168 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain B: P.154, K.155, D.167, H.168 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain C: P.154, K.155, D.167, H.168 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain D: P.154, K.155, D.167, H.168 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain E: P.154, K.155, D.167, H.168 Ligand excluded by PLIP

Links

RCSB   PDBe   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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