SMTL ID : 4x11.1

JC Polyomavirus genotype 3 VP1 in complex with GD1a oligosaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-pentamer

Ligands

3 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.1: 9 residues within 4Å: Chain A: L.37, K.42, S.43, N.106, N.247, S.249, S.251, Q.253 Chain D: F.50 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.37, D:F.50 Hydrogen bonds: A:S.43, A:N.106, A:N.247, A:S.249, A:S.251 Water bridges: A:S.249, D:R.144 SIA.6: 9 residues within 4Å: Chain B: L.37, K.42, S.43, N.106, N.247, S.249, S.251, Q.253 Chain C: F.50 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.37, C:F.50 Hydrogen bonds: B:S.43, B:N.106, B:N.247, B:S.249, B:S.251 Water bridges: B:D.34, B:S.249, C:F.50, C:R.144 SIA.13: 9 residues within 4Å: Chain A: F.50 Chain C: L.37, K.42, S.43, N.106, N.247, S.249, S.251, Q.253 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.37, A:F.50 Hydrogen bonds: C:S.43, C:N.106, C:N.247, C:N.247, C:S.249, C:S.251 Water bridges: C:D.34, C:S.249, A:R.144

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

EDO.2: 4 residues within 4Å: Chain A: H.125, F.127, G.197, T.198 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Water bridges: C:I.211, A:G.197, A:R.259 EDO.3: 6 residues within 4Å: Chain A: E.191, N.192, R.194, D.221, V.225, G.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.191, A:R.194, A:R.194 EDO.7: 7 residues within 4Å: Chain B: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.8, EDO.9 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B Water bridges: E:I.211 Hydrogen bonds: B:G.197 EDO.8: 3 residues within 4Å: Chain B: F.196, T.217 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) EDO.9: 7 residues within 4Å: Chain B: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.210, B:H.210, B:R.259 Water bridges: B:R.259 EDO.11: 6 residues within 4Å: Chain B: E.191, N.192, R.194, D.221, G.226, L.228 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.194, B:R.194, B:V.225, B:L.228 EDO.15: 7 residues within 4Å: Chain C: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.17 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.210, C:H.210, C:R.259 Water bridges: C:R.259 EDO.16: 4 residues within 4Å: Chain C: F.127, F.196, T.217 Ligands: EDO.17 2 PLIP interactions: 2 interactions with chain C Water bridges: C:T.217, C:T.217 EDO.17: 6 residues within 4Å: Chain C: F.127, F.196, G.197, T.198 Ligands: EDO.15, EDO.16 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.198 Water bridges: C:G.197 EDO.18: 6 residues within 4Å: Chain C: E.191, N.192, R.194, D.221, V.225, G.226 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.194, C:R.194, C:V.225 EDO.20: 3 residues within 4Å: Chain D: F.127, G.197, T.198 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Water bridges: A:I.211, A:I.211, D:H.125, D:R.259, D:R.259 EDO.21: 7 residues within 4Å: Chain D: E.191, N.192, R.194, D.221, V.225, G.226, L.228 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.194, D:R.194, D:G.226 EDO.22: 2 residues within 4Å: Chain D: F.196, T.217 No protein-ligand interaction detected (PLIP) EDO.23: 8 residues within 4Å: Chain A: H.104 Chain D: S.45, S.47, S.52, D.53, S.54, P.55, M.59 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.45, D:S.52, D:S.54

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: S.45, S.47, D.53, S.54, P.55, M.59 Chain C: H.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.45, A:S.47, A:S.54 Water bridges: A:N.56 GOL.10: 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.45, B:S.52, B:S.54 Water bridges: B:N.56 GOL.14: 8 residues within 4Å: Chain B: H.104 Chain C: S.45, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.45, C:S.47, C:S.54 Water bridges: C:N.56 GOL.26: 7 residues within 4Å: Chain D: H.104 Chain E: S.45, S.47, S.52, D.53, S.54, P.55 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

6 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: E.51, S.52, D.53, R.144, T.146 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.51, A:R.144, A:T.146, H2O.4 K.12: 5 residues within 4Å: Chain B: E.51, D.53, S.54, R.144, T.146 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.51, B:D.53, B:R.144, B:T.146, H2O.9 K.19: 5 residues within 4Å: Chain C: E.51, S.52, D.53, R.144, T.146 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.51, C:D.53, C:R.144, C:T.146, H2O.17 K.24: 2 residues within 4Å: Chain D: E.23 Chain E: T.188 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: D:E.23, E:T.188, H2O.26, H2O.29 K.25: 5 residues within 4Å: Chain D: E.51, S.52, D.53, R.144, T.146 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.53, D:R.144, D:T.146, H2O.23, H2O.25 K.27: 6 residues within 4Å: Chain E: E.51, S.52, D.53, S.54, R.144, T.146 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.53, E:R.144, E:T.146, H2O.29, H2O.30

Links

RCSB   PDBe   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

2015-05-06

Peptides

Major capsid protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

C
A

D
C

E
D

Major capsid protein

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