SMTL ID : 4jce.1

L54F Variant of JC Polyomavirus Major Capsid Protein VP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-pentamer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: S.45, I.46, S.47, S.52, D.53, S.54, P.55, M.59 Chain E: H.104 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:H.104, A:D.53, A:S.54 Water bridges: A:I.46 GOL.2: 7 residues within 4Å: Chain A: H.104 Chain B: S.45, S.47, S.52, D.53, S.54, P.55 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.53, B:S.54, A:H.104 GOL.3: 6 residues within 4Å: Chain B: V.94, H.125, V.208, L.209, H.210, R.259 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.210, B:R.259 Water bridges: B:R.259 GOL.4: 7 residues within 4Å: Chain B: E.191, N.192, R.194, D.221, G.226, P.227, L.228 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.192, B:R.194, B:R.194, B:D.221 GOL.5: 8 residues within 4Å: Chain B: H.104 Chain C: S.45, S.47, S.52, D.53, S.54, P.55, M.59 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.53, C:S.54 GOL.6: 5 residues within 4Å: Chain C: H.125, F.127, F.196, G.197, T.198 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.197 Water bridges: C:H.125, C:G.197, C:R.259, C:R.259 GOL.7: 8 residues within 4Å: Chain C: H.104 Chain D: S.45, S.47, S.52, D.53, S.54, P.55, M.59 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:H.104, D:D.53, D:S.54 GOL.9: 7 residues within 4Å: Chain D: H.104 Chain E: S.45, S.47, S.52, D.53, S.54, P.55 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:H.104, E:D.53, E:S.54 GOL.11: 7 residues within 4Å: Chain E: S.123, H.125, T.198, P.207, V.208, L.209 Ligands: EDO.10 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:P.206, E:V.208, E:V.208 Water bridges: E:S.123, E:S.123, E:T.200 GOL.12: 8 residues within 4Å: Chain E: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.194, E:R.194, E:G.226

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

EDO.8: 3 residues within 4Å: Chain D: P.69, L.70, P.71 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain E: H.125, F.127, F.196, G.197, T.198 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.198 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