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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-pentamer

Ligands

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

NAG-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 19 PLIP interactions: 2 interactions with chain B, 17 interactions with chain A 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 Water bridges: B:S.50, B:S.51, B:A.53, B:S.51, B:K.52, A:Y.42, A:D.45, A:D.45, A:G.108, A:G.109, A:S.252, A:S.254, A:S.254 Hydrophobic interactions: A:L.39, A:Y.42 NAG-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 17 PLIP interactions: 2 interactions with chain C, 15 interactions with chain B 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 Water bridges: C:S.51, C:A.53, B:S.252, C:S.51, C:K.52, B:Y.42, B:D.45, B:D.45, B:G.108, B:S.252, B:S.254, B:S.254 Hydrophobic interactions: B:L.39, B:Y.42 NAG-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.23 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain E Water bridges: D:S.252, E:S.50, E:S.51, E:A.53, E:K.52, D:D.45, D:D.45, D:G.108, D:G.109, D:S.252, D:S.254, D:S.254, E:K.52 Hydrogen bonds: E:K.52, D:Q.107, D:G.108, D:N.250, D:N.250, D:Y.251, D:N.256, D:N.256 Hydrophobic interactions: D:Y.42 NAG-GAL-SIA.4: 13 residues within 4Å: Chain A: 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 Ligands: EDO.9 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain E Hydrogen bonds: A:K.52, E:Q.107, E:G.108, E:N.250, E:N.250, E:Y.251, E:N.256 Water bridges: A:S.51, A:A.53, E:S.252, E:D.45, E:D.45, E:G.108, E:S.252, E:S.254, A:K.52 Hydrophobic interactions: E:Y.42

5 x CA: CALCIUM ION(Non-covalent)

CA.5: 2 residues within 4Å: Chain A: E.23 Chain B: S.191 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.15 CA.13: 2 residues within 4Å: Chain B: E.23 Chain C: S.191 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:S.191, B:E.23, B:E.23, H2O.27, H2O.28 CA.19: 2 residues within 4Å: Chain C: E.23 Chain D: S.191 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:E.23, D:S.191, H2O.27, H2O.28, H2O.34 CA.22: 2 residues within 4Å: Chain D: E.23 Chain E: S.191 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.45 CA.26: 3 residues within 4Å: Chain A: S.191, E.194 Chain E: E.23 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:E.23, E:E.23, H2O.8, H2O.37, H2O.46

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

EDO.6: 7 residues within 4Å: Chain A: L.167, K.172, D.189, S.191 Chain E: Y.25, M.97, Y.263 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.172, A:S.191 Water bridges: A:K.172, A:S.191 EDO.7: 7 residues within 4Å: Chain A: G.108, G.109, Y.111, Y.251 Chain B: V.48, A.49, S.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.109 EDO.8: 7 residues within 4Å: Chain A: E.194, N.195, R.197, D.224, V.228, G.229, P.230 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.194, A:R.197, A:R.197 Water bridges: A:D.224, A:D.224 EDO.9: 3 residues within 4Å: Chain A: S.51, A.53 Ligands: NAG-GAL-SIA.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.51, A:S.51 Water bridges: A:A.53 EDO.10: 6 residues within 4Å: Chain A: R.197, L.223, D.224 Chain E: K.93, N.216, S.217 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain A Hydrogen bonds: E:K.93, A:L.223 Water bridges: E:K.93, E:N.216, A:R.197, A:R.197, A:R.197, A:E.225 EDO.11: 4 residues within 4Å: Chain A: V.96, H.128, M.212, Q.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.128, A:Q.213, A:Q.213 EDO.14: 7 residues within 4Å: Chain A: Y.25, M.97, Y.263 Chain B: Q.140, K.172, D.189, S.191 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.172, B:S.191 EDO.15: 6 residues within 4Å: Chain B: Y.25, M.97, Y.263 Chain C: L.167, K.172, S.191 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.172, C:S.191 Water bridges: C:K.172, C:S.191 EDO.16: 7 residues within 4Å: Chain A: K.93, N.216, S.217 Chain B: R.197, L.222, L.223, D.224 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.93 Water bridges: B:V.221 EDO.17: 4 residues within 4Å: Chain B: F.130, Y.199, T.220 Ligands: IPA.18 No protein-ligand interaction detected (PLIP) EDO.20: 5 residues within 4Å: Chain C: L.39, Y.42, H.248, N.250, N.256 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.248, C:N.250 Water bridges: C:N.256 EDO.23: 7 residues within 4Å: Chain D: G.108, G.109, Y.111, Y.251 Chain E: A.49, S.50 Ligands: NAG-GAL-SIA.3 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.109, D:G.109 EDO.24: 6 residues within 4Å: Chain D: E.194, N.195, D.224, V.228, G.229, P.230 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.231 EDO.27: 6 residues within 4Å: Chain D: Y.25, Y.263 Chain E: Q.140, L.167, K.172, S.191 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.172, E:K.172, E:S.191 EDO.28: 3 residues within 4Å: Chain E: Y.199, T.220 Ligands: IPA.29 No protein-ligand interaction detected (PLIP)

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

IPA.12: 5 residues within 4Å: Chain A: H.128, F.130, Y.199, G.200, S.201 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.130, A:Y.199 IPA.18: 6 residues within 4Å: Chain B: H.128, F.130, Y.199, G.200, S.201 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.130 IPA.21: 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.25: 6 residues within 4Å: Chain D: H.128, F.130, Y.199, G.200, S.201, R.262 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.130, D:Y.199 IPA.29: 6 residues within 4Å: Chain E: H.128, F.130, Y.199, G.200, S.201 Ligands: EDO.28 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.130

Links

RCSB   PDBe   PDBe-KB   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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