SMTL ID : 6k2o.1

Structural basis of glycan recognition in globally predominant human P[8] rotavirus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

6 x GAL- NAG- GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose

GAL-NAG-GAL-FUC.1: 8 residues within 4Å: Chain A: L.103, R.108, W.110, T.120, T.121, R.145, E.148, N.152 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.121, A:T.121, A:E.148, A:N.152, A:R.145, A:R.145, A:E.148 Water bridges: A:E.148 GAL-NAG-GAL-FUC.3: 8 residues within 4Å: Chain B: L.103, R.108, W.110, T.120, T.121, R.145, E.148, N.152 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.121, B:T.121, B:E.148, B:N.152, B:R.145, B:R.145, B:E.148 Water bridges: B:E.148 GAL-NAG-GAL-FUC.5: 8 residues within 4Å: Chain C: L.103, R.108, W.110, T.120, T.121, R.145, E.148, N.152 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.121, C:T.121, C:E.148, C:N.152, C:R.145, C:R.145, C:E.148 Water bridges: C:E.148 GAL-NAG-GAL-FUC.7: 8 residues within 4Å: Chain D: L.103, R.108, W.110, T.120, T.121, R.145, E.148, N.152 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.121, D:T.121, D:T.121, D:N.152, D:T.121, D:R.145, D:R.145, D:E.148 GAL-NAG-GAL-FUC.9: 8 residues within 4Å: Chain E: L.103, R.108, W.110, T.120, T.121, R.145, E.148, N.152 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.121, E:T.121, E:T.121, E:N.152, E:T.121, E:R.145, E:R.145, E:E.148 GAL-NAG-GAL-FUC.11: 8 residues within 4Å: Chain F: L.103, R.108, W.110, T.120, T.121, R.145, E.148, N.152 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.121, F:T.121, F:T.121, F:N.152, F:T.121, F:R.145, F:R.145, F:E.148

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

NA.2: 2 residues within 4Å: Chain A: R.90, R.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.90, A:R.90, A:R.91 NA.4: 2 residues within 4Å: Chain B: R.90, R.91 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.90, B:R.90, B:R.91 NA.6: 2 residues within 4Å: Chain C: R.90, R.91 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.90, C:R.90, C:R.91 NA.8: 2 residues within 4Å: Chain D: R.90, R.91 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.90, D:R.90, D:R.91 NA.10: 2 residues within 4Å: Chain E: R.90, R.91 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.90, E:R.90, E:R.91 NA.12: 2 residues within 4Å: Chain F: R.90, R.91 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.90, F:R.90, F:R.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, X. et al., Structural Basis of Glycan Recognition in Globally Predominant Human P[8] Rotavirus. Virol Sin (2020)

Release Date

2019-10-09

Peptides

Outer capsid protein VP4: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Outer capsid protein VP4