SMTL ID : 3tay.1 (1 other biounit)

Crystal structure of porcine rotavirus CRW-8 VP8* in complex with N-glycolylneuraminic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 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.40, S.83, H.94, N.117, G.126, Y.127, Y.128, S.129 Ligands: EPE.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.127 Hydrogen bonds: A:R.40, A:R.40, A:S.83, A:S.83, A:N.117, A:Y.127, A:Y.127, A:S.129 Water bridges: A:H.94, A:G.95, A:Y.127, A:Y.127, A:Y.127

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: T.92, Q.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.93 Water bridges: A:Q.93, A:Q.93 SO4.3: 3 residues within 4Å: Chain A: S.73, Q.74, T.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.73, A:Q.74, A:T.75

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 8 residues within 4Å: Chain A: P.25, T.26, V.27, G.29, V.30, V.31, F.141, C.142 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.31 MPD.5: 3 residues within 4Å: Chain A: P.7, Y.8, D.143 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.7 Hydrogen bonds: A:D.143

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 4 residues within 4Å: Chain A: D.39, R.40, T.85 Ligands: MN0.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.40 Salt bridges: A:D.39

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.7: 5 residues within 4Å: Chain A: M.107, Y.114, T.125, R.149, E.152 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.125, A:R.149, A:R.149

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 6 residues within 4Å: Chain A: D.81, G.95, Y.104, T.115, Y.116, N.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.115, A:T.115

Links

RCSB   PDBe   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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