SMTL ID : 4jcf.1

S268F Variant of JC Polyomavirus Major Capsid Protein VP1 in Complex with LSTc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-pentamer

Ligands

1 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA.1: 12 residues within 4Å: Chain A: L.37, K.42, S.43, N.106, N.247, R.248, S.249, F.251, Q.253 Chain D: D.48, T.49, F.50 13 PLIP interactions: 1 interactions with chain C, 10 interactions with chain A, 2 interactions with chain D Water bridges: C:N.113, A:D.34, A:S.43, A:S.43, A:S.249, A:S.249, D:R.144 Hydrogen bonds: A:N.106, A:S.43, A:N.106, A:N.247, A:S.249 Hydrophobic interactions: D:T.49, A:L.37, D:F.50

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: S.45, I.46, S.47, S.52, D.53, S.54, P.55, M.59 Chain C: H.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.45, A:S.54, A:S.54 GOL.3: 9 residues within 4Å: Chain B: S.45, I.46, S.47, S.52, D.53, S.54, P.55, M.59 Chain E: H.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.54, B:S.54 Water bridges: B:I.46, B:N.56 GOL.5: 8 residues within 4Å: Chain B: H.104 Chain C: S.45, I.46, S.47, D.53, S.54, P.55, M.59 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:H.104, C:S.54, C:S.54 Water bridges: C:I.46, C:N.56 GOL.6: 8 residues within 4Å: Chain A: H.104 Chain D: S.45, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.45, D:S.52, D:S.54 Water bridges: D:N.56 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 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.52, E:S.54, D:H.104 Water bridges: E:S.45, E:S.45

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

EDO.4: 3 residues within 4Å: Chain B: H.125, G.197, T.198 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:H.125, B:T.198 Water bridges: B:G.197, E:I.211

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
C

B
A

C
B

D
D

E
E

Major capsid protein VP1