SMTL ID : 4x10.1

JC Polyomavirus genotype 3 VP1 in complex with GM2 oligosaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-pentamer

Ligands

2 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(Non-functional Binders)

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 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain C Hydrogen bonds: 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:S.249, B:S.249, B:S.249, C:F.50 Hydrophobic interactions: B:L.37, 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 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Water bridges: C:S.249, C:S.251, C:S.249, D:F.50 Hydrophobic interactions: C:L.37, D:F.50 Hydrogen bonds: C:S.43, C:N.106, C:N.247, C:N.247, C:S.249, C:S.251, C:S.251

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

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.249, D:S.249, E:F.50 Hydrophobic interactions: D:L.37, E:F.50

15 x GOL: GLYCEROL(Non-functional Binders)(Non-covalent)

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:S.45, A:D.53, A:S.54 GOL.5: 8 residues within 4Å: Chain A: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.194, A:R.194, A:G.226, A:L.228 Water bridges: A:E.191, A:D.221 GOL.6: 6 residues within 4Å: Chain A: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.125, A:T.198, A:T.198 Water bridges: A:H.125, A:G.197, A:G.197 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: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.104, B:S.45, B:S.52, B:S.54 GOL.11: 8 residues within 4Å: Chain B: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.194, B:R.194 Water bridges: B:E.191 GOL.13: 7 residues within 4Å: Chain B: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.12, GOL.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.197 Water bridges: A:I.211 GOL.14: 7 residues within 4Å: Chain B: V.94, H.125, V.208, L.209, H.210, R.259 Ligands: GOL.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.125, B:H.210, B:H.210, B:R.259 Water bridges: B:R.259 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 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.45, C:S.54 Water bridges: C:S.52, C:N.56 GOL.17: 8 residues within 4Å: Chain C: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.194, C:R.194, C:G.226 Water bridges: C:E.191, C:D.221 GOL.18: 6 residues within 4Å: Chain C: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.19 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:F.196, C:T.198, C:T.198 Water bridges: C:G.197, B:I.211 GOL.21: 7 residues within 4Å: Chain C: H.104 Chain D: S.45, S.47, D.53, S.54, P.55, M.59 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.45, D:S.47, D:S.54 Water bridges: D:N.56 GOL.22: 8 residues within 4Å: Chain D: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.194, D:R.194, D:G.226, D:L.228 Water bridges: D:E.191, D:E.191 GOL.23: 5 residues within 4Å: Chain D: H.125, F.127, G.197, T.198 Ligands: EDO.24 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:H.125, D:T.198 Water bridges: D:H.125, D:G.197, C:I.211 GOL.27: 5 residues within 4Å: Chain E: H.125, F.127, G.197, T.198 Ligands: EDO.28 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:H.125, E:T.198 Water bridges: E:G.197, D:I.211 GOL.29: 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:L.228 Water bridges: E:E.191

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

EDO.7: 4 residues within 4Å: Chain A: F.127, F.196, T.217 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.217, A:T.217 EDO.12: 4 residues within 4Å: Chain B: F.127, F.196, T.217 Ligands: GOL.13 No protein-ligand interaction detected (PLIP) EDO.19: 4 residues within 4Å: Chain C: F.127, F.196, T.217 Ligands: GOL.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.217 EDO.24: 4 residues within 4Å: Chain D: F.127, F.196, T.217 Ligands: GOL.23 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.217 EDO.28: 3 residues within 4Å: Chain E: F.196, T.217 Ligands: GOL.27 No protein-ligand interaction detected (PLIP) EDO.30: 5 residues within 4Å: Chain A: S.45, I.46 Chain E: A.109, N.113, G.114 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:N.113, E:N.113, A:I.46, A:I.46

7 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.8: 5 residues within 4Å: Chain A: E.51, S.52, D.53, 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.8 K.9: 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.5, H2O.5, H2O.8 K.15: 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.20: 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.26 K.25: 6 residues within 4Å: Chain D: E.51, S.52, D.53, S.54, 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.34 K.26: 3 residues within 4Å: Chain D: E.23 Chain E: T.188, E.191 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.23, D:E.23, H2O.39, H2O.40, H2O.40 K.31: 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.41

Links

RCSB   PDBe   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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