SMTL ID : 4x13.1

JC Polyomavirus genotype 3 VP1 in complex with LSTc pentasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-pentamer

Ligands

2 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: 11 residues within 4Å: Chain B: L.37, K.42, S.43, N.106, N.247, R.248, S.249, S.251, Q.253 Chain C: D.48, F.50 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain C Water bridges: B:R.248, B:R.248, B:S.43, B:S.249, B:S.251, C:F.50 Hydrogen bonds: B:N.106, B:S.43, B:S.43, 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 BGC-GAL-NAG-GAL-SIA.2: 11 residues within 4Å: Chain C: L.37, K.42, S.43, N.106, N.247, R.248, S.249, S.251, Q.253 Chain D: D.48, F.50 16 PLIP interactions: 12 interactions with chain C, 1 interactions with chain B, 3 interactions with chain D Water bridges: C:R.248, C:R.248, B:N.113, D:F.50, D:R.144, C:S.43, C:S.249, C:S.251 Hydrogen bonds: C:N.106, C:S.43, C:S.43, 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

1 x 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(Non-functional Binders)

GAL-NAG-GAL-SIA.3: 12 residues within 4Å: Chain A: D.48, T.49, F.50 Chain E: L.37, K.42, S.43, N.106, N.247, R.248, S.249, S.251, Q.253 15 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 12 interactions with chain E Water bridges: D:N.113, E:D.34, E:S.43, E:S.43, E:S.43, E:S.43, E:S.249, A:R.144 Hydrophobic interactions: A:T.49, E:L.37, A:F.50 Hydrogen bonds: E:N.106, E:S.43, E:N.106, E:N.247, E:S.249, E:S.251

11 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 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:S.54, E:H.104 Water bridges: A:D.48, A:D.48 GOL.8: 8 residues within 4Å: Chain A: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.194, A:R.194, A:G.226 GOL.15: 8 residues within 4Å: Chain B: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.191, B:R.194, B:R.194, B:D.221 GOL.16: 7 residues within 4Å: Chain A: H.104 Chain B: S.45, S.47, D.53, S.54, P.55, M.59 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.45, B:D.53, B:S.54, B:N.56 GOL.19: 7 residues within 4Å: Chain B: H.104 Chain C: S.45, S.47, D.53, S.54, P.55, M.59 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.45, C:S.54, C:S.54 Water bridges: C:D.48, C:S.52, C:N.56 GOL.21: 6 residues within 4Å: Chain C: H.125, F.127, F.196, G.197, T.198 Ligands: EDO.20 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.197 GOL.22: 8 residues within 4Å: Chain C: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.191, C:R.194, C:R.194, C:D.221 GOL.24: 8 residues within 4Å: Chain C: H.104 Chain D: S.45, S.47, S.52, D.53, S.54, P.55, M.59 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.53, D:S.54 Water bridges: D:D.48 GOL.25: 8 residues within 4Å: Chain D: E.191, N.192, R.194, D.221, V.225, G.226, P.227, L.228 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.194, D:R.194 Water bridges: D:E.191 GOL.27: 5 residues within 4Å: Chain D: H.125, F.127, G.197, T.198 Ligands: EDO.26 4 PLIP interactions: 4 interactions with chain D Water bridges: D:H.125, D:G.197, D:G.197, D:R.259 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:N.192, E:R.194, E:R.194, E:D.221

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

EDO.5: 3 residues within 4Å: Chain A: F.127, T.217 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.217 Water bridges: A:T.217 EDO.6: 6 residues within 4Å: Chain A: H.125, F.127, G.197, T.198 Ligands: EDO.5, EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.198 Water bridges: A:G.197, A:G.197 EDO.7: 5 residues within 4Å: Chain A: V.94, H.125, L.209, R.259 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.259 Water bridges: A:H.125, A:V.208, A:R.259 EDO.10: 4 residues within 4Å: Chain B: F.127, F.196, T.217 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.217 EDO.11: 6 residues within 4Å: Chain B: H.125, F.196, G.197, T.198 Ligands: EDO.10, EDO.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.197 Water bridges: B:G.197 EDO.12: 5 residues within 4Å: Chain B: V.94, H.125, L.209, R.259 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.125, B:R.259, B:R.259 EDO.13: 5 residues within 4Å: Chain B: A.109, N.113, G.114 Chain C: S.45, I.46 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.113, B:G.114, C:I.46 EDO.14: 4 residues within 4Å: Chain A: T.214 Chain B: L.220, D.221, E.222 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:T.214, B:V.218 Hydrogen bonds: B:D.221 EDO.17: 2 residues within 4Å: Chain B: T.214 Chain C: E.222 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.214 EDO.20: 4 residues within 4Å: Chain C: F.127, F.196, T.217 Ligands: GOL.21 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.217 EDO.26: 3 residues within 4Å: Chain D: F.196, T.217 Ligands: GOL.27 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.217 EDO.30: 4 residues within 4Å: Chain E: F.127, F.196, T.217 Ligands: EDO.31 No protein-ligand interaction detected (PLIP) EDO.31: 5 residues within 4Å: Chain E: H.125, F.127, G.197, T.198 Ligands: EDO.30 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Water bridges: D:I.211, E:G.197 EDO.32: 4 residues within 4Å: Chain D: T.214 Chain E: L.220, D.221, E.222 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Water bridges: D:T.214, E:V.218 EDO.33: 7 residues within 4Å: Chain D: H.104 Chain E: S.45, S.47, S.52, D.53, S.54, P.55 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:H.104, E:S.52, E:S.54

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

K.9: 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.7 K.18: 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.15 K.23: 6 residues within 4Å: Chain C: E.51, S.52, D.53, S.54, R.144, T.146 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.51, C:D.53, C:R.144, C:T.146, H2O.22, H2O.22 K.28: 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.31 K.34: 5 residues within 4Å: Chain E: E.51, S.52, D.53, R.144, T.146 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.51, E:D.53, E:R.144, E:T.146

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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