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

Structure of unliganded VP1 pentamer of Human Polyomavirus 9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-pentamer

Ligands

5 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: E.23 Chain B: S.191, E.194 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:S.191, A:E.23, H2O.4, H2O.8, H2O.16 CA.4: 3 residues within 4Å: Chain B: E.23 Chain C: S.191, E.194 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:S.191, B:E.23, H2O.16, H2O.18, H2O.20 CA.7: 3 residues within 4Å: Chain C: E.23 Chain D: S.191, E.194 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:E.23, C:E.23, D:S.191, H2O.30, H2O.30 CA.10: 2 residues within 4Å: Chain D: E.23 Chain E: S.191 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: D:E.23, E:S.191, H2O.37 CA.13: 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.8, H2O.38

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

EDO.2: 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.5: 4 residues within 4Å: Chain B: V.96, H.128, M.212, Q.213 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.128, B:Q.213, B:Q.213 EDO.8: 4 residues within 4Å: Chain C: V.96, H.128, M.212, Q.213 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.128, C:Q.213 EDO.11: 4 residues within 4Å: Chain D: V.96, H.128, M.212, Q.213 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.128, D:Q.213 Water bridges: D:V.211 EDO.14: 4 residues within 4Å: Chain E: V.96, H.128, M.212, Q.213 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:H.128, E:Q.213, E:Q.213 Water bridges: E:Q.213

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

IPA.3: 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.6: 4 residues within 4Å: Chain B: H.128, F.130, Y.199, S.201 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.130 IPA.9: 5 residues within 4Å: Chain C: H.128, F.130, Y.199, G.200, S.201 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.130 Water bridges: C:R.262 IPA.12: 7 residues within 4Å: Chain D: H.128, M.129, F.130, Y.199, G.200, S.201, R.262 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.130 IPA.15: 6 residues within 4Å: Chain E: H.128, F.130, Y.199, G.200, S.201, R.262 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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