SMTL ID : 3nxd.2 (1 other biounit)

JC polyomavirus VP1 in complex with LSTc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-10-mer

Ligands

4 x BGC- GAL- NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-functional Binders)

BGC-GAL-NAG-GAL-SIA.1: 12 residues within 4Å: Chain A: L.37, K.42, S.43, N.106, N.247, R.248, S.249, S.251, Q.253 Chain D: D.48, T.49, F.50 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain D Water bridges: A:R.248, A:R.248, A:R.248, A:S.249, D:F.50 Hydrophobic interactions: D:T.49, A:L.37, D:F.50 Hydrogen bonds: A:N.106, A:S.43, A:S.43, A:S.43, A:N.106, A:N.247, A:N.247, A:S.249, A:S.251 BGC-GAL-NAG-GAL-SIA.2: 12 residues within 4Å: Chain A: D.48, T.49, F.50 Chain B: L.37, K.42, S.43, N.106, N.247, R.248, S.249, S.251, Q.253 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Water bridges: B:R.248, B:R.248, B:S.43, B:S.43, B:S.249, B:S.249, A:F.50 Hydrogen bonds: B:N.106, B:S.43, B:N.106, B:N.247, B:N.247, B:S.249, B:S.251 Hydrophobic interactions: A:T.49, B:L.37, A:F.50 BGC-GAL-NAG-GAL-SIA.14: 12 residues within 4Å: Chain F: L.37, K.42, S.43, N.106, N.247, R.248, S.249, S.251, Q.253 Chain I: D.48, T.49, F.50 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain I Water bridges: F:R.248, F:R.248, F:R.248, F:S.249, I:F.50 Hydrogen bonds: F:N.106, F:S.43, F:S.43, F:S.43, F:N.106, F:N.247, F:N.247, F:S.249, F:S.251 Hydrophobic interactions: I:T.49, F:L.37, I:F.50 BGC-GAL-NAG-GAL-SIA.15: 12 residues within 4Å: Chain F: D.48, T.49, F.50 Chain G: L.37, K.42, S.43, N.106, N.247, R.248, S.249, S.251, Q.253 13 PLIP interactions: 11 interactions with chain G, 2 interactions with chain F Water bridges: G:R.248, G:R.248, F:F.50, G:S.43, G:S.43, G:S.249, G:S.249 Hydrogen bonds: G:N.106, G:S.43, G:N.106, G:N.247, G:N.247, G:S.249, G:S.251 Hydrophobic interactions: F:T.49, F:F.50, G:L.37

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: S.45, S.47, S.52, D.53, S.54, P.55 Chain B: H.104 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.104, A:D.53, A:S.54 GOL.5: 7 residues within 4Å: Chain B: S.45, S.47, S.52, D.53, S.54, P.55 Chain C: H.104 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.53, B:S.54, C:H.104 GOL.6: 7 residues within 4Å: Chain C: S.45, S.47, S.52, D.53, S.54, P.55 Chain E: H.104 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:D.53, C:S.54, E:H.104 GOL.9: 8 residues within 4Å: Chain A: H.104 Chain D: S.45, S.47, S.52, D.53, S.54, P.55, M.59 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:S.45, D:S.54, A:H.104 GOL.11: 7 residues within 4Å: Chain D: H.104 Chain E: S.45, S.47, S.52, D.53, S.54, P.55 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.47, E:D.53, E:S.54, D:H.104 GOL.16: 7 residues within 4Å: Chain F: S.45, S.47, S.52, D.53, S.54, P.55 Chain G: H.104 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:D.53, F:D.53, F:S.54, G:H.104 GOL.18: 7 residues within 4Å: Chain G: S.45, S.47, S.52, D.53, S.54, P.55 Chain H: H.104 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:D.53, G:D.53, G:S.54, H:H.104 GOL.19: 7 residues within 4Å: Chain H: S.45, S.47, S.52, D.53, S.54, P.55 Chain J: H.104 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain J Hydrogen bonds: H:D.53, H:D.53, H:S.54, J:H.104 GOL.22: 8 residues within 4Å: Chain F: H.104 Chain I: S.45, S.47, S.52, D.53, S.54, P.55, M.59 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain F Hydrogen bonds: I:S.45, I:D.53, I:S.54, F:H.104 GOL.24: 7 residues within 4Å: Chain I: H.104 Chain J: S.45, S.47, S.52, D.53, S.54, P.55 5 PLIP interactions: 1 interactions with chain I, 4 interactions with chain J Hydrogen bonds: I:H.104, J:S.47, J:D.53, J:D.53, J:S.54

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

EDO.4: 5 residues within 4Å: Chain A: H.125, F.127, F.196, G.197, T.198 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.197, A:G.197 EDO.7: 3 residues within 4Å: Chain C: H.125, F.127, T.198 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.125, C:T.198 Water bridges: C:G.197, C:G.197 EDO.8: 6 residues within 4Å: Chain C: V.94, H.125, V.208, L.209, H.210, R.259 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.208, C:H.210, C:R.259 EDO.10: 4 residues within 4Å: Chain D: H.125, F.127, G.197, T.198 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.125 Water bridges: D:G.197, D:G.197 EDO.12: 6 residues within 4Å: Chain E: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain E Water bridges: E:G.197, E:G.197 EDO.13: 4 residues within 4Å: Chain E: F.127, F.196, T.217 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.217, E:T.217 EDO.17: 5 residues within 4Å: Chain F: H.125, F.127, F.196, G.197, T.198 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.198 Water bridges: F:G.197, F:G.197 EDO.20: 3 residues within 4Å: Chain H: H.125, F.127, T.198 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:H.125 Water bridges: H:G.197, H:G.197 EDO.21: 6 residues within 4Å: Chain H: V.94, H.125, V.208, L.209, H.210, R.259 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:V.208, H:H.210, H:R.259 EDO.23: 4 residues within 4Å: Chain I: H.125, F.127, G.197, T.198 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:H.125, I:T.198 Water bridges: I:G.197, I:G.197 EDO.25: 6 residues within 4Å: Chain J: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.26 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:T.198 Water bridges: J:G.197, J:G.197 EDO.26: 4 residues within 4Å: Chain J: F.127, F.196, T.217 Ligands: EDO.25 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:T.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neu, U. et al., Structure-function analysis of the human JC polyomavirus establishes the LSTc pentasaccharide as a functional receptor motif. Cell Host Microbe (2010)

Release Date

2010-11-17

Peptides

Major capsid protein VP1: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

D
D

E
E

F
C

G
B

H
A

I
D

J
E

Major capsid protein VP1

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