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

Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-pentamer

Ligands

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

BGC-GAL-SIA.1: 13 residues within 4Å: Chain A: L.39, Y.42, D.45, Q.107, G.108, G.109, H.248, N.250, Y.251, N.256 Chain B: S.50, S.51, K.52 15 PLIP interactions: 1 interactions with chain B, 14 interactions with chain A Water bridges: B:S.51, B:K.52, B:S.50, B:S.51, B:A.53, A:S.252, A:D.45, A:D.45, A:G.108, A:S.252, A:S.254, A:S.254, B:K.52 Hydrogen bonds: B:K.52, A:Q.107, A:G.108, A:N.250, A:N.250, A:N.250, A:Y.251, A:N.256 Hydrophobic interactions: A:Y.42 BGC-GAL-SIA.2: 13 residues within 4Å: Chain B: L.39, Y.42, D.45, Q.107, G.108, G.109, H.248, N.250, Y.251, N.256 Chain C: S.50, S.51, K.52 18 PLIP interactions: 4 interactions with chain C, 14 interactions with chain B Water bridges: C:S.51, C:K.52, C:S.51, C:A.53, B:Y.42, B:D.45, B:D.45, B:G.108, B:S.252, B:S.254, B:S.254 Hydrogen bonds: C:S.50, C:K.52, B:Q.107, B:G.108, B:N.250, B:Y.251, B:N.256, B:N.256 Hydrophobic interactions: B:Y.42 BGC-GAL-SIA.3: 14 residues within 4Å: Chain D: L.39, Y.42, D.45, Q.107, G.108, G.109, H.248, N.250, Y.251, N.256 Chain E: S.50, S.51, K.52 Ligands: EDO.25 17 PLIP interactions: 4 interactions with chain E, 13 interactions with chain D Water bridges: E:K.52, E:S.50, E:S.51, E:A.53, D:D.45, D:G.108, D:G.109, D:S.252, D:S.254 Hydrogen bonds: E:K.52, D:S.252, D:D.45, D:Q.107, D:G.108, D:N.250, D:Y.251, D:N.256, D:N.256 Hydrophobic interactions: D:Y.42 BGC-GAL-SIA.4: 13 residues within 4Å: Chain A: S.50, S.51, K.52 Chain E: L.39, Y.42, D.45, Q.107, G.108, G.109, H.248, N.250, Y.251, N.256 15 PLIP interactions: 1 interactions with chain A, 14 interactions with chain E Water bridges: A:K.52, E:S.252, E:D.45, E:D.45, E:G.108, E:S.252, E:S.254, E:S.254, A:K.52 Hydrogen bonds: A:S.50, A:K.52, E:Q.107, E:G.108, E:N.250, E:Y.251, E:N.256, E:N.256 Hydrophobic interactions: E:L.39, E:Y.42

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: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.23, A:E.23, B:S.191, H2O.7, H2O.10 CA.10: 3 residues within 4Å: Chain B: E.23 Chain C: S.191, E.194 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:S.191, B:E.23, B:E.23, H2O.28 CA.15: 3 residues within 4Å: Chain C: E.23 Chain D: S.191, E.194 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:S.191, C:E.23, H2O.29 CA.21: 3 residues within 4Å: Chain D: E.23 Chain E: S.191, E.194 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:S.191, D:E.23, D:E.23, H2O.40 CA.27: 3 residues within 4Å: Chain A: S.191, E.194 Chain E: E.23 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: A:S.191, E:E.23, E:E.23, H2O.1, H2O.7

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

EDO.6: 4 residues within 4Å: Chain A: V.96, H.128, M.212, Q.213 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: G.108, G.109, Y.111, Y.251 Chain B: V.48, A.49, S.50 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: P.169, K.172, S.191 Chain E: Y.25, M.97, Y.263 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: V.96, H.128, M.212, Q.213 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: Y.25, Y.263 Chain B: L.167, K.172, S.191 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain A: K.93, S.217 Chain B: R.197, Y.199, V.221, L.222, L.223, D.224 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain C: V.96, H.128, M.212, Q.213 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain B: Y.25, M.97, Y.263 Chain C: Q.140, L.167, K.172, D.189, S.191 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain C: G.108, G.109, Y.111, Y.251 Chain D: V.48, A.49, S.50 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: G.108, G.109, Y.111, Y.251 Chain C: V.48, A.49, S.50 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain D: V.96, H.128, M.212, Q.213 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain C: Y.25, M.97, Y.263 Chain D: K.172, D.189, S.191 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain C: K.93, N.216, S.217 Chain D: R.197, Y.199, V.221, L.223, D.224 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain D: G.108, G.109, Y.111, Y.251 Chain E: A.49, S.50 Ligands: BGC-GAL-SIA.3 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain E: V.96, H.128, M.212, Q.213 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain A: V.48, A.49, S.50 Chain E: G.108, G.109, Y.111, Y.251 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain D: Y.25, M.97, Y.263 Chain E: L.167, K.172, S.191 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain E: Y.25, L.26, N.27, R.29, Y.40 Ligand excluded by PLIP

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

IPA.9: 5 residues within 4Å: Chain A: H.128, F.130, Y.199, G.200, S.201 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.130 IPA.14: 5 residues within 4Å: Chain B: H.128, F.130, Y.199, G.200, S.201 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.130 Water bridges: B:H.128 IPA.20: 6 residues within 4Å: Chain C: H.128, M.129, F.130, Y.199, G.200, S.201 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:H.128, C:F.130, C:F.130 Hydrogen bonds: C:S.201 IPA.26: 5 residues within 4Å: Chain D: H.128, F.130, Y.199, G.200, S.201 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.130, D:Y.199 IPA.32: 5 residues within 4Å: Chain E: H.128, F.130, Y.199, G.200, S.201 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.130 Hydrogen bonds: E:H.128

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Khan, Z.M. et al., Crystallographic and glycan microarray analysis of human polyomavirus 9 VP1 identifies N-glycolyl neuraminic acid as a receptor candidate. J.Virol. (2014)

Release Date

2014-04-09

Peptides

VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

VP1

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