SMTL ID : 4x0z.1

JC Polyomavirus genotype 3 VP1 in complex with GM1 oligosaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-pentamer

Ligands

2 x GAL- NGA- GAL- SIA: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose

GAL-NGA-GAL-SIA.1: 12 residues within 4Å: Chain A: N.113 Chain B: L.37, K.42, S.43, I.44, N.106, N.247, S.249, S.251, Q.253 Chain C: F.50 Ligands: EDO.11 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.43, B:I.44, B:K.42, B:K.42, B:S.43, B:N.106, B:N.247, B:N.247, B:S.249, B:S.251, B:S.251 Water bridges: B:Q.252, B:S.249, C:F.50 Hydrophobic interactions: B:L.37, C:F.50 GAL-NGA-GAL-SIA.2: 13 residues within 4Å: Chain B: N.113 Chain C: L.37, K.42, S.43, I.44, S.45, N.106, N.247, S.249, S.251, Q.253 Chain D: F.50 Ligands: EDO.19 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.43, C:S.43, C:K.42, C:S.43, C:N.106, C:N.247, C:S.249, C:S.251, C:S.251 Water bridges: C:S.45, C:S.249, C:S.249, C:S.249, D:F.50 Hydrophobic interactions: C:L.37, D:F.50

1 x BGC- GAL- NGA- GAL- SIA: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-NGA-GAL-SIA.3: 12 residues within 4Å: Chain C: N.113 Chain D: L.37, K.42, S.43, I.44, S.45, N.106, N.247, S.249, S.251, Q.253 Chain E: F.50 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:S.43, D:I.44, D:K.42, D:S.43, D:N.106, D:N.247, D:N.247, D:S.249, D:S.251 Water bridges: D:S.249, D:S.249, D:S.249, E:F.50 Hydrophobic interactions: D:L.37, E:F.50

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: E.191, R.194, D.221, E.222, F.223 Ligands: GOL.7 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: L.220, D.221, E.222 Chain E: T.214 Ligand excluded by PLIP GOL.6: 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.7: 9 residues within 4Å: Chain A: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 Ligands: GOL.4 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.9 Ligand excluded by PLIP GOL.15: 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.17: 5 residues within 4Å: Chain B: E.191, R.194, D.221, F.223 Ligands: GOL.18 Ligand excluded by PLIP GOL.18: 9 residues within 4Å: Chain B: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 Ligands: GOL.17 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain C: T.214 Chain D: L.220, D.221, E.222 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain C: E.191, R.194, D.221, E.222, F.223 Ligands: GOL.26 Ligand excluded by PLIP GOL.25: 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.26: 9 residues within 4Å: Chain C: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 Ligands: GOL.24 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain C: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.28, GOL.30 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain C: H.125, T.198, T.200, V.208, L.209 Ligands: EDO.28, GOL.29 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain C: H.104 Chain D: S.45, S.47, D.53, S.54, P.55, M.59 Ligand excluded by PLIP GOL.34: 9 residues within 4Å: Chain D: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 Ligands: GOL.35 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain D: E.191, R.194, D.221, E.222, F.223 Ligands: GOL.34 Ligand excluded by PLIP GOL.41: 5 residues within 4Å: Chain E: E.191, R.194, D.221, F.223 Ligands: GOL.43 Ligand excluded by PLIP GOL.42: 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 GOL.43: 9 residues within 4Å: Chain E: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 Ligands: GOL.41 Ligand excluded by PLIP GOL.46: 6 residues within 4Å: Chain E: H.125, F.127, G.197, T.198 Ligands: EDO.44, GOL.47 Ligand excluded by PLIP GOL.47: 7 residues within 4Å: Chain E: H.125, T.198, T.200, V.208, L.209, H.210 Ligands: GOL.46 Ligand excluded by PLIP

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

EDO.8: 4 residues within 4Å: Chain A: F.127, F.196, T.217 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.217 EDO.9: 6 residues within 4Å: Chain A: H.125, F.127, G.197, T.198 Ligands: EDO.8, GOL.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:H.125, A:T.198 Water bridges: A:G.197, E:I.211 EDO.11: 6 residues within 4Å: Chain A: A.109, N.113, G.114 Chain B: S.45, I.46 Ligands: GAL-NGA-GAL-SIA.1 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.113, A:N.113, B:I.46, B:I.46 EDO.16: 4 residues within 4Å: Chain B: F.127, F.196, T.217 Ligands: EDO.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.217 EDO.19: 6 residues within 4Å: Chain B: A.109, N.113, G.114 Chain C: S.45, I.46 Ligands: GAL-NGA-GAL-SIA.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.113, B:N.113, C:I.46, C:I.46 EDO.20: 6 residues within 4Å: Chain B: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.16 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:G.197, A:I.211 EDO.27: 4 residues within 4Å: Chain C: F.127, F.196, T.217 Ligands: EDO.28 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.217 EDO.28: 6 residues within 4Å: Chain C: H.125, G.197, T.198 Ligands: EDO.27, GOL.29, GOL.30 No protein-ligand interaction detected (PLIP) EDO.36: 5 residues within 4Å: Chain D: H.125, F.127, G.197, T.198 Ligands: EDO.38 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.125 Water bridges: D:G.197, D:G.197 EDO.37: 4 residues within 4Å: Chain D: T.214 Chain E: L.220, D.221, E.222 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:D.221 Water bridges: E:V.218, D:T.214, D:T.214 EDO.38: 4 residues within 4Å: Chain D: F.127, F.196, T.217 Ligands: EDO.36 No protein-ligand interaction detected (PLIP) EDO.44: 4 residues within 4Å: Chain E: F.127, F.196, T.217 Ligands: GOL.46 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.217 EDO.45: 5 residues within 4Å: Chain A: S.45, I.46 Chain E: A.109, N.113, G.114 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:N.113, A:I.46 Water bridges: E:H.111

10 x K: POTASSIUM ION(Non-covalent)

K.12: 3 residues within 4Å: Chain A: T.188, E.191 Chain E: E.23 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: E:E.23, E:E.23, A:E.191, H2O.7, H2O.8 K.13: 3 residues within 4Å: Chain A: E.23 Chain B: T.188, E.191 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:E.191, H2O.17, H2O.18 K.14: 6 residues within 4Å: Chain A: E.51, S.52, D.53, S.54, R.144, T.146 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.53, A:R.144, A:T.146, H2O.2, H2O.3 K.21: 3 residues within 4Å: Chain B: E.23 Chain C: T.188, E.191 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:E.23, B:E.23, C:T.188, C:E.191, H2O.18 K.22: 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.16 K.31: 3 residues within 4Å: Chain C: E.23 Chain D: T.188, E.191 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:E.23, C:E.23, D:E.191, H2O.36, H2O.37 K.32: 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.27 K.39: 3 residues within 4Å: Chain D: E.23 Chain E: T.188, E.191 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: D:E.23, D:E.23, E:E.191, H2O.37, H2O.48 K.40: 5 residues within 4Å: Chain D: E.51, S.52, D.53, R.144, T.146 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.51, D:D.53, D:R.144, D:T.146, H2O.38 K.48: 5 residues within 4Å: Chain E: E.51, S.52, 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.48

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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