SMTL ID : 4mbz.1 (1 other biounit)

Structure of B-Lymphotropic Polyomavirus VP1 in complex with 3'-sialyllactosamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-pentamer

Ligands

4 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)(Non-functional Binders)

GAL-SIA.1: 11 residues within 4Å: Chain A: L.39, Y.42, Q.107, G.108, H.248, N.250, Y.251, V.256 Chain B: F.50, S.51, K.52 16 PLIP interactions: 4 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:K.52, A:Q.107, A:G.108, A:H.248, A:N.250, A:N.250, A:Y.251 Water bridges: B:F.50, B:S.51, B:A.53, A:S.45, A:G.108, A:N.250, A:S.252 Hydrophobic interactions: A:Y.42, A:V.256 GAL-SIA.2: 12 residues within 4Å: Chain B: L.39, Y.42, S.45, Q.107, G.108, H.248, N.250, Y.251, V.256 Chain C: F.50, S.51, K.52 13 PLIP interactions: 1 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:K.52, B:Q.107, B:G.108, B:H.248, B:N.250, B:N.250, B:Y.251, C:K.52 Water bridges: C:F.50, C:S.51, C:A.53, B:Y.42, B:S.45, B:G.108, B:S.252 Hydrophobic interactions: B:Y.42, B:V.256 GAL-SIA.3: 12 residues within 4Å: Chain D: L.39, Y.42, Q.107, G.108, G.109, H.248, N.250, Y.251, V.256 Chain E: F.50, S.51, K.52 13 PLIP interactions: 1 interactions with chain E, 12 interactions with chain D Hydrogen bonds: E:K.52, D:Q.107, D:G.108, D:H.248, D:N.250, D:Y.251 Water bridges: E:F.50, E:S.51, E:A.53, D:S.45, D:G.108, D:N.250, D:S.252, E:K.52 Hydrophobic interactions: D:L.39, D:Y.42, D:V.256 GAL-SIA.4: 12 residues within 4Å: Chain A: F.50, S.51, K.52 Chain E: L.39, Y.42, Q.107, G.108, G.109, H.248, N.250, Y.251, V.256 16 PLIP interactions: 1 interactions with chain A, 15 interactions with chain E Hydrogen bonds: A:K.52, E:Q.107, E:G.108, E:G.108, E:H.248, E:N.250, E:N.250, E:Y.251 Water bridges: A:F.50, A:S.51, E:G.108, E:N.250, E:N.250, E:N.250, E:S.252, A:K.52 Hydrophobic interactions: E:L.39, E:Y.42, E:V.256

5 x CA: CALCIUM ION(Non-functional Binders)

CA.5: 3 residues within 4Å: Chain A: E.23 Chain B: S.191, E.194 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.23, B:S.191, H2O.15, H2O.26, H2O.27 CA.10: 3 residues within 4Å: Chain B: E.23 Chain C: S.191, E.194 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:E.23, C:S.191, H2O.27, H2O.37, H2O.39 CA.18: 3 residues within 4Å: Chain C: E.23 Chain D: S.191, E.194 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: D:S.191, C:E.23, H2O.38, H2O.40, H2O.47 CA.23: 3 residues within 4Å: Chain D: E.23 Chain E: S.191, E.194 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:S.191, H2O.59, H2O.63 CA.28: 3 residues within 4Å: Chain A: S.191, E.194 Chain E: E.23 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: E:E.23, A:S.191, H2O.1, H2O.1, H2O.14

5 x CL: CHLORIDE ION(Non-covalent)(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: I.157, K.158, A.171, W.186 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: I.157, K.158, A.171, W.186 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain C: I.157, K.158, K.170, A.171 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain D: I.157, K.158, A.171, W.186 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain E: I.157, K.158, K.170, A.171, W.186 Ligand excluded by PLIP

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

EDO.7: 8 residues within 4Å: Chain A: E.194, N.195, R.197, D.224, V.228, G.229, P.230, L.231 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.197, A:R.197, A:D.224 Water bridges: A:N.195 EDO.8: 4 residues within 4Å: Chain A: T.94, F.130, R.262 Ligands: IPA.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.262, A:R.262 Water bridges: A:V.96, A:Q.213, A:Q.213 EDO.12: 4 residues within 4Å: Chain B: N.32, E.37, N.44, D.60 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.44, B:D.60, B:D.60 Water bridges: B:N.32 EDO.13: 4 residues within 4Å: Chain B: L.75, N.76, G.234, D.235 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.75, B:N.76, B:N.76, B:N.76 Water bridges: B:G.234 EDO.14: 5 residues within 4Å: Chain B: T.94, F.130, R.262 Ligands: EDO.15, IPA.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.262, B:R.262 Water bridges: B:V.96, B:Q.213 EDO.15: 5 residues within 4Å: Chain B: V.96, H.128, M.212, Q.213 Ligands: EDO.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.128, B:Q.213 Water bridges: B:V.211, B:Q.213 EDO.16: 7 residues within 4Å: Chain B: E.194, N.195, R.197, D.224, V.228, G.229, P.230 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.197, B:R.197, B:D.224, B:G.229 EDO.20: 5 residues within 4Å: Chain C: L.75, N.76, M.79, G.234, D.235 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.75, C:N.76, C:N.76, C:D.235 Water bridges: C:G.234 EDO.21: 5 residues within 4Å: Chain C: N.32, E.37, N.44, K.59, D.60 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.44, C:D.60, C:D.60 Water bridges: C:N.32 EDO.25: 5 residues within 4Å: Chain D: L.75, N.76, M.79, G.234, D.235 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.75, D:N.76, D:N.76, D:N.76 EDO.26: 5 residues within 4Å: Chain D: T.94, F.130, Q.213, R.262 Ligands: IPA.27 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.213, D:R.262, D:R.262 Water bridges: D:V.96 EDO.30: 4 residues within 4Å: Chain E: T.94, F.130, R.262 Ligands: IPA.33 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.213, E:R.262, E:R.262 Water bridges: E:V.96 EDO.31: 5 residues within 4Å: Chain E: N.195, L.231, K.233, P.276 Ligands: EDO.32 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.233 EDO.32: 8 residues within 4Å: Chain E: E.194, N.195, R.197, D.224, V.228, G.229, L.231 Ligands: EDO.31 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.197, E:R.197, E:D.224, E:V.228

5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)(Non-covalent)

IPA.9: 6 residues within 4Å: Chain A: H.128, F.130, Y.199, G.200, S.201 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.128, A:F.130 Hydrogen bonds: A:G.200 Water bridges: A:G.200 IPA.17: 6 residues within 4Å: Chain B: H.128, F.130, Y.199, G.200, S.201 Ligands: EDO.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.130 Water bridges: B:S.201, B:R.262 IPA.22: 5 residues within 4Å: Chain C: H.128, F.130, Y.199, G.200, S.201 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.130 IPA.27: 6 residues within 4Å: Chain D: H.128, F.130, Y.199, G.200, S.201 Ligands: EDO.26 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.130 Water bridges: D:R.262 IPA.33: 6 residues within 4Å: Chain E: H.128, F.130, Y.199, G.200, S.201 Ligands: EDO.30 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.130 Water bridges: E:R.262

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Neu, U. et al., Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands. Plos Pathog. (2013)

Release Date

2013-12-04

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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