SMTL ID : 2i2s.2 (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: 2 residues within 4Å: Chain A: Y.8, Q.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.9 Water bridges: A:P.7

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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.95, A:Y.104 Water bridges: A:D.81

1 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, Y.127, Y.128, S.129 Ligands: GOL.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: 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:H.94, A:Y.127

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.149, N.150, E.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.149 GOL.5: 1 residues within 4Å: Ligands: MNA.3 No protein-ligand interaction detected (PLIP)

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

MPD.6: 2 residues within 4Å: Chain A: T.75, Q.76 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.75 Hydrogen bonds: A:T.75 Water bridges: A:T.75, A:Q.76

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
B

Outer capsid protein VP4

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