SMTL ID : 4x15.1

JC Mad-1 polyomavirus VP1 in complex with GM2 oligosaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-pentamer

Ligands

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

BGC-GAL-SIA-NGA.1: 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: 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: 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 Water bridges: B:S.249, C:F.50 BGC-GAL-SIA-NGA.2: 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 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.42, C:S.43, C:N.106, C:N.247, C:N.247, C:S.249, C:S.251 Hydrophobic interactions: D:F.50, C:L.37 Water bridges: D:F.50, C:S.249 BGC-GAL-SIA-NGA.3: 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 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain E Hydrogen bonds: 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.251, D:S.249, E:F.50 Hydrophobic interactions: D:L.37, E:F.50

7 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.53, A:S.54 Water bridges: A:N.56 GOL.6: 6 residues within 4Å: Chain A: E.191, N.192, R.194, D.221, G.226, P.227 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.194, A:R.194, A:G.226 Water bridges: A:N.192 GOL.10: 9 residues within 4Å: Chain A: H.104 Chain B: S.45, I.46, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.54, A:H.104 Water bridges: B:S.52, B:N.56 GOL.13: 8 residues within 4Å: Chain B: H.104 Chain C: S.45, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.45, C:D.53, C:S.54 Water bridges: C:N.56 GOL.18: 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 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.53, D:S.54 GOL.21: 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.23: 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.52, E:S.54, D:H.104 Water bridges: E:N.56

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

EDO.5: 3 residues within 4Å: Chain A: F.127, T.217 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.217 EDO.7: 6 residues within 4Å: Chain A: V.94, H.125, V.208, L.209, H.210, R.259 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.125, A:H.210, A:H.210, A:R.259 EDO.8: 5 residues within 4Å: Chain A: H.125, F.127, G.197, T.198 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.198 Water bridges: A:G.197, A:G.197 EDO.11: 4 residues within 4Å: Chain B: F.127, F.196, T.217 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.217 EDO.12: 6 residues within 4Å: Chain B: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.11 No protein-ligand interaction detected (PLIP) EDO.14: 6 residues within 4Å: Chain C: H.125, F.127, G.197, T.198 Ligands: EDO.15, EDO.16 2 PLIP interactions: 2 interactions with chain C Water bridges: C:G.197, C:G.197 EDO.15: 4 residues within 4Å: Chain C: F.127, F.196, T.217 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.217, C:T.217 EDO.16: 7 residues within 4Å: Chain C: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.210, C:R.259 EDO.17: 7 residues within 4Å: Chain C: E.191, N.192, R.194, D.221, V.225, G.226, L.228 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.191, C:R.194, C:R.194 EDO.19: 4 residues within 4Å: Chain D: H.125, F.127, G.197, T.198 2 PLIP interactions: 2 interactions with chain D Water bridges: D:G.197, D:G.197 EDO.20: 6 residues within 4Å: Chain D: V.94, H.125, V.208, L.209, H.210, R.259 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.208, D:H.210, D:R.259 EDO.24: 3 residues within 4Å: Chain E: F.196, T.217 Ligands: EDO.25 No protein-ligand interaction detected (PLIP) EDO.25: 6 residues within 4Å: Chain E: H.125, F.196, G.197, T.198 Ligands: EDO.24, EDO.26 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.197 Water bridges: E:G.197 EDO.26: 7 residues within 4Å: Chain E: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: EDO.25 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:H.125, E:H.210, E:H.210, E:R.259 Water bridges: E:R.259

2 x K: POTASSIUM ION(Non-covalent)

K.9: 3 residues within 4Å: Chain A: T.188, E.191 Chain E: E.23 5 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: E:E.23, A:T.188, A:E.191, H2O.5, H2O.34 K.22: 3 residues within 4Å: Chain D: E.23 Chain E: T.188, E.191 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:T.188, E:E.191, D:E.23, D:E.23, H2O.32

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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