SMTL ID : 4x16.1

JC Mad-1 polyomavirus VP1 in complex with GD1a oligosaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-pentamer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: S.45, S.47, S.52, D.53, S.54, P.55, M.59 Chain E: H.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.45, A:S.54 Water bridges: A:S.52, A:N.56 GOL.6: 8 residues within 4Å: Chain A: H.104 Chain B: S.45, S.47, S.52, D.53, S.54, P.55, M.59 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.52, B:S.54, A:H.104 GOL.9: 8 residues within 4Å: Chain B: S.123, H.125, T.198, P.207, V.208, L.209 Ligands: EDO.7, EDO.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.206, B:V.208, B:V.208 Water bridges: B:S.123, B:S.123, B:T.200 GOL.12: 9 residues within 4Å: Chain B: H.104 Chain C: S.45, I.46, S.47, S.52, D.53, S.54, P.55, M.59 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.54 Water bridges: C:S.52, C:N.56 GOL.14: 7 residues within 4Å: Chain C: S.123, H.125, T.198, T.200, P.207, V.208, L.209 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:P.206, C:V.208, C:V.208 Water bridges: C:S.123, C:S.123, C:H.125 GOL.16: 9 residues within 4Å: Chain C: H.104 Chain D: S.45, I.46, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.54 Water bridges: D:I.46, D:S.52, D:N.56 GOL.18: 8 residues within 4Å: Chain D: H.104 Chain E: S.45, S.47, S.52, D.53, S.54, P.55, M.59 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.52, E:S.54, D:H.104 GOL.20: 7 residues within 4Å: Chain E: H.125, T.198, T.200, P.207, V.208, L.209 Ligands: EDO.19 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:V.208, E:V.208 Water bridges: E:S.123, E:S.123, E:H.125, E:P.206 GOL.21: 5 residues within 4Å: Chain A: S.45, I.46 Chain E: A.109, N.113, G.114 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:I.46, A:I.46, E:N.113, E:N.113

6 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.125, A:T.198 Water bridges: A:G.197, A:G.197 EDO.7: 7 residues within 4Å: Chain B: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.8, GOL.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.125 Water bridges: B:G.197, B:G.197 EDO.8: 7 residues within 4Å: Chain B: H.125, V.208, L.209, H.210, R.259 Ligands: EDO.7, GOL.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.208, B:H.210, B:R.259 EDO.13: 4 residues within 4Å: Chain C: H.125, F.127, G.197, T.198 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.125 Water bridges: C:G.197, C:G.197 EDO.17: 4 residues within 4Å: Chain D: H.125, F.127, G.197, T.198 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.125 Water bridges: D:G.197, D:G.197 EDO.19: 6 residues within 4Å: Chain E: H.125, V.208, L.209, H.210, R.259 Ligands: GOL.20 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.210, E:H.210, E:R.259

3 x K: POTASSIUM ION(Non-covalent)

K.3: 2 residues within 4Å: Chain A: E.23 Chain B: T.188 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:T.188, A:E.23, H2O.3, H2O.15 K.4: 2 residues within 4Å: Chain A: T.188 Chain E: E.23 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: A:T.188, E:E.23, H2O.6, H2O.8, H2O.40 K.10: 2 residues within 4Å: Chain B: E.23 Chain C: T.188 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.23, H2O.24, H2O.24

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

SIA.5: 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 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:F.50, B:L.37 Water bridges: C:F.50, C:R.144, B:S.249 Hydrogen bonds: B:S.43, B:S.43, B:S.43, B:N.106, B:N.247, B:S.249, B:S.251 SIA.11: 9 residues within 4Å: Chain C: L.37, K.42, S.43, N.106, N.247, S.249, S.251, Q.253 Chain D: F.50 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.37, D:F.50 Hydrogen bonds: C:S.43, C:N.106, C:N.247, C:N.247, C:S.249, C:S.251, C:S.251 Water bridges: C:N.106, C:S.249, D:F.50 SIA.15: 9 residues within 4Å: Chain D: L.37, K.42, S.43, N.106, N.247, S.249, S.251, Q.253 Chain E: F.50 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:L.37, E:F.50 Hydrogen bonds: D:S.43, D:N.106, D:N.247, D:N.247, D:S.249, D:S.251, D:S.251 Water bridges: D:D.34, D:S.249, E:R.144

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 VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Major capsid protein VP1

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