SMTL ID : 4jcd.1

S268Y Variant of JC Polyomavirus Major Capsid Protein VP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-pentamer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: S.45, S.47, S.52, D.53, S.54, P.55 Chain E: H.104 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:H.104, A:D.53, A:S.54 GOL.3: 9 residues within 4Å: Chain A: H.104 Chain B: S.45, I.46, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.104, B:S.54, B:S.54 Water bridges: B:N.56 GOL.4: 8 residues within 4Å: Chain B: H.104 Chain C: S.45, I.46, S.47, S.52, D.53, S.54, P.55 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.45, C:D.53, C:S.54, B:H.104 Water bridges: C:I.46 GOL.5: 7 residues within 4Å: Chain C: H.104 Chain D: S.45, S.47, S.52, D.53, S.54, P.55 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.45, D:S.54, C:H.104 Water bridges: D:S.54, D:S.54 GOL.7: 8 residues within 4Å: Chain D: H.104 Chain E: S.45, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.45, E:S.52, E:S.54, D:H.104

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

EDO.2: 5 residues within 4Å: Chain A: H.125, F.127, F.196, G.197, T.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.198 Water bridges: A:G.197, A:G.197 EDO.6: 4 residues within 4Å: Chain D: H.125, F.127, G.197, T.198 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Water bridges: D:G.197, C:I.211 EDO.8: 5 residues within 4Å: Chain E: H.125, F.127, F.196, G.197, T.198 2 PLIP interactions: 2 interactions with chain E Water bridges: E:G.197, E:G.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maginnis, M.S. et al., Progressive multifocal leukoencephalopathy-associated mutations in the JC polyomavirus capsid disrupt lactoseries tetrasaccharide c binding. MBio (2013)

Release Date

2013-08-14

Peptides

Major capsid protein VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Major capsid protein VP1