SMTL ID : 5caz.1

Crystallographic structure of apo human rotavirus K8 VP8*

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

7 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.1: 3 residues within 4Å: Chain A: P.23, T.24, R.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.24, A:R.25, A:R.25 IPA.2: 1 residues within 4Å: Chain A: Q.61 No protein-ligand interaction detected (PLIP) IPA.3: 4 residues within 4Å: Chain A: N.69, D.70, S.71, K.76 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.70 Hydrogen bonds: A:N.69, A:D.70 IPA.4: 4 residues within 4Å: Chain A: Y.92, S.93, T.94, Q.115 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.94 Hydrogen bonds: A:T.94, A:T.94 IPA.5: 4 residues within 4Å: Chain A: N.51, T.52, Q.53, H.66 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.51, A:Q.53 Hydrogen bonds: A:Q.53 IPA.6: 5 residues within 4Å: Chain A: K.82, L.83, T.84, G.87, T.88 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.84 Hydrogen bonds: A:L.83 IPA.7: 2 residues within 4Å: Chain A: R.54, Q.55 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.55 Hydrogen bonds: A:Q.55, A:Q.55

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

SO4.8: 3 residues within 4Å: Chain A: V.49, T.52, R.54 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.50, A:T.52, A:R.54 Salt bridges: A:R.54

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 9 residues within 4Å: Chain A: C.42, F.77, L.79, S.93, T.94, L.95, W.113, Y.114, Q.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.93, A:Y.114 Water bridges: A:A.103

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
A

Outer capsid protein VP4

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