SMTL ID : 2i2s.1 (1 other biounit)

Crystal Structure of the porcine CRW-8 rotavirus VP8* carbohydrate-recognising domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: G.29, V.30, Y.58, N.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.30, A:I.57, A:N.59, A:N.59

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

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

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

MNA.3: 7 residues within 4Å: Chain A: R.40, S.83, H.94, N.117, Y.127, Y.128, S.129 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.127, A:Y.128 Hydrogen bonds: A:R.40, A:R.40, A:S.83, A:S.83, A:Y.127, A:S.129 Water bridges: A:H.94, A:H.94, A:Y.127, A:Y.127 MNA.4: 7 residues within 4Å: Chain A: T.53, S.68, V.69, E.70, Y.91, T.92, Q.93 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.53 Hydrogen bonds: A:S.68, A:Q.93 Water bridges: A:S.68, A:S.68, A:S.68, A:E.70, A:Y.91, A:Q.93, A:Q.93, A:Q.93

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

MPD.5: 5 residues within 4Å: Chain A: W.41, F.61, Q.63, K.84, P.87 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.61, A:Q.63, A:P.87 Hydrogen bonds: A:W.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blanchard, H. et al., Insight into Host Cell Carbohydrate-recognition by Human and Porcine Rotavirus from Crystal Structures of the Virion Spike Associated Carbohydrate-binding Domain (VP8*). J.Mol.Biol. (2007)

Release Date

2007-04-03

Peptides

Outer capsid protein VP4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Outer capsid protein VP4

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