SMTL ID : 2aen.1

Crystal structure of the rotavirus strain DS-1 VP8* core

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-octamer

Ligands

4 x EOH: ETHANOL(Non-functional Binders)

EOH.1: 8 residues within 4Å: Chain A: W.22, L.108, W.115, E.153 Chain D: Y.110, W.115, R.150 Ligands: GOL.5 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:Y.110, D:R.150, A:E.153 Hydrophobic interactions: A:L.108, A:W.115 EOH.4: 4 residues within 4Å: Chain B: Y.110, W.115, R.150 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.115 Hydrogen bonds: B:R.150 EOH.9: 4 residues within 4Å: Chain G: Y.110, W.115, R.150 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:W.115 Hydrogen bonds: G:R.150 EOH.10: 8 residues within 4Å: Chain E: Y.110, W.115, R.150 Chain H: W.22, L.108, W.115, E.153 Ligands: GOL.6 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain H Hydrogen bonds: E:Y.110, E:R.150, H:E.153 Hydrophobic interactions: H:L.108, H:W.115

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain B: L.108, Y.110, W.115, T.126, R.150, E.153 Ligands: EOH.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.126, B:T.126, B:R.150, B:R.150 Water bridges: B:E.153, B:E.153 GOL.3: 3 residues within 4Å: Chain B: N.30, E.50, R.58 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.30 Water bridges: B:N.30 GOL.5: 9 residues within 4Å: Chain A: R.150, E.153 Chain D: L.108, Y.110, W.115, T.126, R.150, E.153 Ligands: EOH.1 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:T.126, D:R.150, A:R.150, A:R.150 GOL.6: 9 residues within 4Å: Chain E: L.108, Y.110, W.115, T.126, R.150, E.153 Chain H: R.150, E.153 Ligands: EOH.10 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain E Hydrogen bonds: H:R.150, H:R.150, E:T.126, E:R.150, E:R.150 GOL.7: 7 residues within 4Å: Chain G: L.108, Y.110, W.115, T.126, R.150, E.153 Ligands: EOH.9 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:T.126, G:T.126, G:R.150, G:R.150 Water bridges: G:E.153, G:E.153 GOL.8: 3 residues within 4Å: Chain G: N.30, E.50, R.58 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:N.30, G:E.50 Water bridges: G:N.30

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Monnier, N. et al., High-resolution molecular and antigen structure of the VP8* core of a sialic acid-independent human rotavirus strain. J.Virol. (2006)

Release Date

2006-02-07

Peptides

Outer capsid protein VP4, VP8* core: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Outer capsid protein VP4, VP8* core