SMTL ID : 4x14.1

JC Mad-1 polyomavirus VP1 in complex with GM1 oligosaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-pentamer

Ligands

1 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, S.45, N.106, N.247, S.249, S.251, Q.253 Chain C: F.50 13 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B, 2 interactions with chain C Water bridges: A:N.113, A:N.113, B:S.249, B:S.249, C:F.50 Hydrogen bonds: B:S.43, B:S.43, B:K.42, B:K.42, B:S.43, B:N.106, B:N.247, B:N.247, B:S.249, B:S.251 Hydrophobic interactions: B:L.37, C:F.50

2 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.2: 12 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 13 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: C:K.42, C:K.42, C:S.43, B:N.113, C:S.43, C:N.106, C:N.247, C:N.247, C:S.249, C:S.251 Water bridges: B:N.113, C:S.249, D:F.50, D:R.144 Hydrophobic interactions: C:L.37, D:F.50 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 12 PLIP interactions: 2 interactions with chain C, 8 interactions with chain D, 2 interactions with chain E Hydrogen bonds: C:N.113, D:S.43, D:S.43, D:N.106, D:N.247, D:N.247, D:S.249, D:S.251 Water bridges: C:N.113, D:S.249, E:F.50 Hydrophobic interactions: D:L.37, E:F.50

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: S.45, S.47, S.52, D.53, S.54, P.55, M.59 Chain E: H.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.54 Water bridges: A:N.56 GOL.11: 8 residues within 4Å: Chain A: H.104 Chain B: S.45, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.104, B:S.45, B:S.54 Water bridges: B:N.56 GOL.16: 8 residues within 4Å: Chain B: H.104 Chain C: S.45, S.47, S.52, D.53, S.54, P.55, M.59 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:H.104, C:S.54 GOL.21: 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.45, D:S.54, C:H.104 GOL.25: 8 residues within 4Å: Chain D: H.104 Chain E: S.45, S.47, S.52, D.53, S.54, P.55, M.59 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.45, E:S.45, E:S.54, D:H.104 Water bridges: E:N.56

15 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.210, A:H.210, A:R.259 Water bridges: A:R.259 EDO.6: 3 residues within 4Å: Chain A: F.127, T.217 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.217 EDO.7: 5 residues within 4Å: Chain A: H.125, G.197, T.198 Ligands: EDO.5, EDO.6 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Water bridges: E:I.211, A:G.197 Hydrogen bonds: A:T.198 EDO.8: 7 residues within 4Å: Chain A: E.191, N.192, R.194, D.221, V.225, G.226, L.228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.191, A:R.194, A:R.194 EDO.12: 4 residues within 4Å: Chain B: F.127, F.196, T.217 Ligands: EDO.13 No protein-ligand interaction detected (PLIP) EDO.13: 6 residues within 4Å: Chain B: H.125, F.196, G.197, T.198 Ligands: EDO.12, EDO.14 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:I.211, B:G.197 EDO.14: 6 residues within 4Å: Chain B: H.125, V.208, L.209, H.210, R.259 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.210, B:H.210, B:R.259 EDO.17: 4 residues within 4Å: Chain C: H.125, G.197, T.198 Ligands: EDO.18 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:I.211, C:G.197 EDO.18: 4 residues within 4Å: Chain C: F.127, F.196, T.217 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.217 EDO.19: 6 residues within 4Å: Chain C: E.191, N.192, R.194, D.221, V.225, G.226 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.192, C:R.194, C:R.194, C:D.221 EDO.22: 4 residues within 4Å: Chain D: H.125, F.196, G.197, T.198 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:I.211 Hydrogen bonds: D:G.197 EDO.23: 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:E.191, D:R.194, D:R.194 EDO.26: 4 residues within 4Å: Chain E: F.127, F.196, T.217 Ligands: EDO.28 No protein-ligand interaction detected (PLIP) EDO.27: 6 residues within 4Å: Chain E: L.26, T.27, E.29, S.64, V.65, N.175 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.27, E:E.29, E:E.29 EDO.28: 5 residues within 4Å: Chain E: H.125, F.196, G.197, T.198 Ligands: EDO.26 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:F.196 Water bridges: E:H.125, E:G.197, E:R.259

5 x K: POTASSIUM ION(Non-covalent)

K.9: 3 residues within 4Å: Chain A: E.23 Chain B: T.188, E.191 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:T.188, B:E.191, A:E.23, H2O.5, H2O.9 K.10: 3 residues within 4Å: Chain A: T.188, E.191 Chain E: E.23 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: A:T.188, A:E.191, E:E.23, E:E.23, H2O.5 K.15: 3 residues within 4Å: Chain B: E.23 Chain C: T.188, E.191 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:E.23, C:T.188, H2O.10, H2O.13 K.20: 3 residues within 4Å: Chain C: E.23 Chain D: T.188, E.191 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:T.188, D:E.191, C:E.23, H2O.16, H2O.20 K.24: 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.24, H2O.25

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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