SMTL ID : 3tb0.1

Crystal structure of Rhesus Rotavirus VP8* in complex with N-Glycolylneuraminic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x MN0: methyl 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid(Non-covalent)

MN0.1: 9 residues within 4Å: Chain A: R.38, V.81, T.83, Y.92, G.93, K.124, Y.125, Y.126, S.127 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.125 Hydrogen bonds: A:R.38, A:R.38, A:Y.125, A:S.127 Water bridges: A:G.93, A:Y.125

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: M.105, H.107, Y.112, T.123, R.147, E.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.123, A:R.147, A:R.147 GOL.3: 4 residues within 4Å: Chain A: S.71, Q.72, T.73, Q.96 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.72, A:T.73, A:T.73, A:Q.74

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 5 residues within 4Å: Chain A: Y.6, F.11, Y.17, F.142, I.144 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, X. et al., Structural Basis of Rotavirus Strain Preference toward N-Acetyl- or N-Glycolylneuraminic Acid-Containing Receptors. J.Virol. (2012)

Release Date

2012-10-17

Peptides

Outer capsid protein VP4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Outer capsid protein VP4

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