SMTL ID : 4x0y.1

JC polyomavirus VP1 from a genotype 3 strain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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, M.59 Chain E: H.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.45, A:S.52, A:S.54 Water bridges: A:D.48 GOL.9: 8 residues within 4Å: Chain A: H.104 Chain B: S.45, 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 Water bridges: B:S.52, B:N.56 GOL.15: 6 residues within 4Å: Chain C: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.13 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.125, C:T.198 Water bridges: C:G.197, C:G.197 GOL.21: 8 residues within 4Å: Chain C: H.104 Chain D: S.45, S.47, S.52, D.53, S.54, P.55, M.59 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.45, D:S.54 Water bridges: D:S.52, D:S.52, D:N.56 GOL.28: 7 residues within 4Å: Chain D: H.104 Chain E: S.45, S.47, S.52, D.53, S.54, P.55 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:H.104, E:S.54, E:S.54 Water bridges: E:I.46, E:I.46

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

EDO.2: 6 residues within 4Å: Chain A: H.125, F.127, G.197, T.198 Ligands: EDO.3, EDO.4 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: F.196, T.217 Ligands: EDO.2 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.2 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: E.191, N.192, R.194, D.221, V.225, G.226, L.228 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain B: F.196, T.217 Ligands: EDO.8 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain B: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.7 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain B: E.191, N.192, R.194, D.221, V.225, G.226, L.228 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: T.214 Chain C: L.220, D.221, E.222 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain C: F.196, T.217 Ligands: GOL.15 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain C: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain C: A.109, N.113, G.114 Chain D: S.45, I.46 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain D: H.125, G.197, T.198 Ligands: EDO.19, EDO.22 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain D: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.18 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain D: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain D: F.127, T.217 Ligands: EDO.18 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain D: T.214 Chain E: D.221, E.222 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain E: F.127, F.196, T.217 Ligands: EDO.27 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain E: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain E: H.125, F.127, G.197, T.198 Ligands: EDO.25 Ligand excluded by PLIP

5 x K: POTASSIUM ION(Non-covalent)

K.6: 5 residues within 4Å: Chain A: E.51, D.53, S.54, R.144, T.146 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.51, A:D.53, A:R.144, A:T.146, H2O.6, H2O.6 K.12: 4 residues within 4Å: Chain B: E.51, D.53, R.144, T.146 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.51, B:D.53, B:R.144, B:T.146, H2O.14, H2O.18 K.17: 5 residues within 4Å: Chain C: E.51, S.52, D.53, R.144, T.146 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.53, C:R.144, C:T.146, H2O.25, H2O.27 K.24: 4 residues within 4Å: Chain D: E.51, D.53, R.144, T.146 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.51, D:D.53, D:R.144, D:T.146, H2O.35, H2O.36 K.29: 4 residues within 4Å: Chain E: E.51, D.53, R.144, T.146 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.51, E:D.53, E:R.144, E:T.146, H2O.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stroh, L.J. et al., The Greater Affinity of JC Polyomavirus Capsid for alpha 2,6-Linked Lactoseries Tetrasaccharide c than for Other Sialylated Glycans Is a Major Determinant of Infectivity. J.Virol. (2015)

Release Date

2015-04-22

Peptides

Major capsid protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Major capsid protein

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