SMTL ID : 5cb7.2 (1 other biounit)

Crystallographic structure of human rotavirus K8 VP8* in complex with A-type HBGA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x GLA- FUC- A2G: alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose

GLA-FUC-A2G.1: 9 residues within 4Å: Chain A: R.38, S.124, Y.125, Y.126, L.127, T.128 Ligands: A2G.2, GAL.3, FUC.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.127 Hydrogen bonds: A:R.38, A:T.128, A:T.128, A:S.124, A:Y.125 Water bridges: A:R.38, A:Y.125, A:Y.125

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.2: 10 residues within 4Å: Chain A: R.38, Y.125, Y.126, L.127, T.128 Ligands: GLA-FUC-A2G.1, GLA-FUC-A2G.1, GLA-FUC-A2G.1, GAL.3, FUC.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.38, A:T.128, A:T.128 Water bridges: A:R.38

1 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.3: 8 residues within 4Å: Chain A: S.124, Y.125, Y.126 Ligands: GLA-FUC-A2G.1, GLA-FUC-A2G.1, GLA-FUC-A2G.1, A2G.2, FUC.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.124, A:Y.125, A:Y.125, A:Y.126

1 x FUC: alpha-L-fucopyranose(Non-functional Binders)

FUC.4: 5 residues within 4Å: Ligands: GLA-FUC-A2G.1, GLA-FUC-A2G.1, GLA-FUC-A2G.1, A2G.2, GAL.3 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: W.18, M.105, R.107, D.108, Y.112, E.123, Q.147 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.107, A:R.107, A:Q.147 Water bridges: A:T.150 GOL.6: 6 residues within 4Å: Chain A: M.105, R.107, D.108, Y.112, Q.147 Ligands: GOL.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.107, A:R.107, A:Q.147 Water bridges: A:E.123, A:E.123, A:E.123

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain A: P.98, H.99, T.118, P.119, N.158 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: Q.53, H.66 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, X. et al., Substantial Receptor-induced Structural Rearrangement of Rotavirus VP8*: Potential Implications for Cross-Species Infection. Chembiochem (2015)

Release Date

2016-06-08

Peptides

Outer capsid protein VP4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Outer capsid protein VP4

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