SMTL ID : 4x17.1

JC Mad-1 polyomavirus VP1 in complex with GD1b oligosaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-pentamer

Ligands

2 x SIA- SIA: N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA-SIA.1: 10 residues within 4Å: Chain B: N.113 Chain C: L.37, K.42, S.43, N.106, N.247, S.249, S.251, Q.253 Chain D: F.50 14 PLIP interactions: 2 interactions with chain D, 12 interactions with chain C Hydrophobic interactions: D:F.50, C:L.37 Water bridges: D:F.50, C:N.106, C:S.249 Hydrogen bonds: C:S.43, C:S.43, C:S.43, C:N.106, C:N.247, C:N.247, C:S.249, C:S.251, C:S.251 SIA-SIA.2: 10 residues within 4Å: Chain C: N.113 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:S.43, D:S.43, D:N.106, D:N.247, D:N.247, D:S.249, D:S.251 Water bridges: D:S.249, E:F.50

17 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.5, GOL.6 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: S.123, H.125, T.198, P.207, V.208, L.209 Ligands: GOL.4 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: S.45, S.47, S.52, D.53, S.54, P.55, M.59 Chain E: H.104 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain B: H.125, T.198, T.200, P.207, V.208, L.209 Ligands: EDO.10 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain A: H.104 Chain B: S.45, S.47, S.52, D.53, S.54, P.55, M.59 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain C: E.191, N.192, R.194, D.221, V.225, G.226, P.227 Ligand excluded by PLIP GOL.17: 8 residues within 4Å: Chain C: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.14, EDO.16, GOL.18 Ligand excluded by PLIP GOL.18: 8 residues within 4Å: Chain C: H.125, T.198, T.200, P.207, V.208, L.209 Ligands: EDO.14, GOL.17 Ligand excluded by PLIP GOL.19: 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 Ligand excluded by PLIP GOL.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 GOL.21: 6 residues within 4Å: Chain D: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.22 Ligand excluded by PLIP GOL.23: 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 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain E: V.65, A.66, R.67, D.173, N.175 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain E: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.26, GOL.28 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain E: H.125, T.198, T.200, P.207, V.208, L.209 Ligands: GOL.27 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain D: H.104 Chain E: S.45, S.47, S.52, D.53, S.54, P.55, M.59 Ligand excluded by PLIP

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

EDO.5: 4 residues within 4Å: Chain A: F.127, F.196, T.217 Ligands: GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.217 EDO.10: 7 residues within 4Å: Chain B: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.11, GOL.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.125 EDO.11: 4 residues within 4Å: Chain B: F.127, F.196, T.217 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.217 EDO.14: 7 residues within 4Å: Chain C: H.125, V.208, L.209, H.210, R.259 Ligands: GOL.17, GOL.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.208, C:H.210, C:R.259 EDO.16: 4 residues within 4Å: Chain C: F.127, F.196, T.217 Ligands: GOL.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.217 Water bridges: C:T.217 EDO.22: 3 residues within 4Å: Chain D: F.127, T.217 Ligands: GOL.21 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.217 EDO.26: 4 residues within 4Å: Chain E: F.127, F.196, T.217 Ligands: GOL.27 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.217

2 x K: POTASSIUM ION(Non-covalent)

K.8: 2 residues within 4Å: Chain A: T.188 Chain E: E.23 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: E:E.23, A:T.188, H2O.6, H2O.8, H2O.37 K.24: 2 residues within 4Å: Chain D: E.23 Chain E: T.188 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: E:T.188, D:E.23, H2O.31, H2O.40, H2O.44

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

SIA.9: 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 10 PLIP interactions: 3 interactions with chain C, 7 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:N.106, B:N.247, B:S.249, B:S.251

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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