SMTL ID : 4x12.1

JC Polyomavirus genotype 3 VP1 in complex with GD1b oligosaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-pentamer

Ligands

3 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 A: L.37, K.42, S.43, N.106, N.247, S.249, S.251, Q.253 Chain B: F.50 Chain E: N.113 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.37, B:F.50 Hydrogen bonds: A:S.43, A:S.43, A:S.43, A:N.106, A:N.247, A:N.247, A:S.249, A:S.251 Water bridges: A:N.106, A:S.249, B:F.50 SIA-SIA.2: 10 residues within 4Å: Chain A: N.113 Chain B: L.37, K.42, S.43, N.106, N.247, S.249, S.251, Q.253 Chain C: F.50 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.43, B:N.106, B:N.247, B:N.247, B:S.249, B:S.251 Water bridges: B:S.249, C:F.50 Hydrophobic interactions: C:F.50 SIA-SIA.3: 10 residues within 4Å: Chain A: F.50 Chain D: N.113 Chain E: L.37, K.42, S.43, N.106, N.247, S.249, S.251, Q.253 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:L.37, A:F.50 Hydrogen bonds: E:S.43, E:N.106, E:N.247, E:N.247, E:S.249, E:S.251 Water bridges: E:S.249, A:F.50

9 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 E: H.104 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain A Hydrogen bonds: E:H.104, A:S.45, A:S.47, A:S.54 Water bridges: A:N.56 GOL.12: 7 residues within 4Å: Chain A: H.104 Chain B: S.45, S.47, D.53, S.54, P.55, M.59 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.45, B:S.47, B:D.53, B:S.54 Water bridges: B:N.56 GOL.14: 8 residues within 4Å: Chain B: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.194, B:R.194, B:L.228 Water bridges: B:E.191 GOL.16: 5 residues within 4Å: Chain B: H.125, F.127, G.197, T.198 Ligands: EDO.15 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.198 Water bridges: B:G.197, A:I.211 GOL.23: 8 residues within 4Å: Chain C: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.194, C:R.194 Water bridges: C:E.191, C:D.221 GOL.26: 8 residues within 4Å: Chain C: H.104 Chain D: S.45, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.45, D:S.52, D:S.54, C:H.104 GOL.29: 8 residues within 4Å: Chain D: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.194, D:R.194 GOL.38: 7 residues within 4Å: Chain D: H.104 Chain E: S.45, S.47, S.52, D.53, S.54, P.55 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:D.53, E:S.54, D:H.104 GOL.39: 8 residues within 4Å: Chain E: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.194, E:R.194, E:G.226, E:L.228

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

EDO.5: 6 residues within 4Å: Chain A: H.125, V.208, L.209, H.210, R.259 Ligands: EDO.7 Ligand excluded by PLIP EDO.6: 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: 6 residues within 4Å: Chain A: H.125, F.127, G.197, T.198 Ligands: EDO.5, EDO.8 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: F.196, T.217 Ligands: EDO.7 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain B: F.153, P.154, K.155, E.167, H.168, K.169, A.170, W.183 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: F.127, F.196, T.217 Ligands: GOL.16 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain C: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.20 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain C: H.125, G.197, T.198 Ligands: EDO.19, EDO.21 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain C: F.196, T.217 Ligands: EDO.20 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain B: H.104 Chain C: S.45, S.47, S.52, D.53, S.54, P.55, M.59 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain D: F.127, T.217 Ligands: EDO.31 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain D: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.30, EDO.31 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain D: H.125, T.198, T.200, V.208, L.209 Ligands: EDO.28 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain D: H.125, F.127, G.197, T.198 Ligands: EDO.27, EDO.28 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain D: P.154, K.155, E.167, H.168, K.169, W.183 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain E: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.36 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain E: H.125, F.127, G.197, T.198 Ligands: EDO.35, EDO.37 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain E: F.127, F.196, T.217 Ligands: EDO.36 Ligand excluded by PLIP

10 x K: POTASSIUM ION(Non-covalent)

K.9: 2 residues within 4Å: Chain A: E.23 Chain B: T.188 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.23, A:E.23, B:T.188, H2O.11, H2O.15 K.10: 6 residues within 4Å: Chain A: E.51, S.52, D.53, S.54, R.144, T.146 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.51, A:D.53, A:R.144, A:T.146, H2O.4 K.11: 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.7, H2O.7, H2O.35 K.17: 3 residues within 4Å: Chain B: E.23 Chain C: T.188, E.191 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:T.188, C:E.191, B:E.23, H2O.10, H2O.20 K.18: 5 residues within 4Å: Chain B: E.51, S.52, D.53, 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.12 K.24: 2 residues within 4Å: Chain C: E.23 Chain D: T.188 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:E.23, D:T.188, H2O.28, H2O.29, H2O.32 K.25: 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.21, H2O.24 K.33: 2 residues within 4Å: Chain D: E.23 Chain E: T.188 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:T.188, D:E.23, H2O.37 K.34: 6 residues within 4Å: Chain D: E.51, S.52, D.53, S.54, 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.26, H2O.31 K.40: 5 residues within 4Å: Chain E: E.51, D.53, S.54, 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.35

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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