SMTL ID : 6y66.2 (1 other biounit)

Structure of Goose Hemorrhagic Polyomavirus VP1 in complex with 2-O-Methyl-5-N-acetyl-alpha-D-neuraminic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-pentamer

Ligands

5 x MNA: 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid(Non-covalent)

MNA.1: 6 residues within 4Å: Chain A: T.58, V.59, A.60, D.66, V.67, P.68 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain A Water bridges: E:R.122, E:R.122, A:V.59 Hydrogen bonds: A:T.58, A:T.58, A:V.67 MNA.4: 7 residues within 4Å: Chain B: T.58, V.59, A.60, D.66, V.67, P.68, P.69 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.58, B:T.58, B:V.67 Water bridges: B:V.59 MNA.8: 6 residues within 4Å: Chain C: T.58, V.59, A.60, D.66, V.67, P.68 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.58, C:T.58, C:V.67 Water bridges: C:V.59, B:R.122, B:R.122 MNA.11: 7 residues within 4Å: Chain D: T.58, V.59, A.60, D.66, V.67, P.68, P.69 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Water bridges: C:R.122, D:V.59, D:V.59 Hydrogen bonds: D:T.58, D:T.58, D:V.67 MNA.13: 7 residues within 4Å: Chain E: T.58, V.59, A.60, D.66, V.67, P.68, P.69 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:T.58, E:T.58, E:V.67 Water bridges: E:V.59, E:V.59, D:R.122

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

EDO.2: 5 residues within 4Å: Chain A: H.139, F.141, F.210, G.211, T.212 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.274, A:R.274 EDO.3: 3 residues within 4Å: Chain A: G.125, G.126, Y.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.125 EDO.6: 5 residues within 4Å: Chain B: L.86, N.87, M.90, G.245, D.246 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.86, B:N.87, B:N.87, B:G.245 Water bridges: B:D.246, B:D.246 EDO.7: 2 residues within 4Å: Chain B: G.126, Y.127 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.126 EDO.9: 4 residues within 4Å: Chain C: G.28, V.29, R.30, L.284 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.30, C:R.30 Water bridges: C:G.28, C:V.29, C:T.31 EDO.10: 2 residues within 4Å: Chain C: G.126, Y.127 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.126 EDO.12: 5 residues within 4Å: Chain D: V.103, K.104, T.105, V.229, T.231 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.103, D:T.105 Water bridges: D:T.105, D:V.229 EDO.14: 4 residues within 4Å: Chain E: R.30, T.92, E.94, L.284 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.30, E:R.30, E:T.92 EDO.15: 3 residues within 4Å: Chain E: G.125, G.126, Y.127 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.125

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 4 residues within 4Å: Chain B: Y.127 Chain C: Y.263, S.264, Q.265 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C pi-Stacking: B:Y.127 Hydrogen bonds: C:S.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stroh, L.J. et al., Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family. Mbio (2020)

Release Date

2020-07-08

Peptides

Capsid protein VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
FFF

B
GGG

C
HHH

D
III

E
JJJ

Capsid protein VP1

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