SMTL ID : 5f4o.1

Protruding domain of GII.17 norovirus Kawasaki308

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: P.7, L.9, E.233, H.237 Chain B: Q.236, Q.240 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.236 Hydrogen bonds: A:H.237 EDO.2: 4 residues within 4Å: Chain A: Q.179, W.180, I.225, D.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.179, A:W.180 Water bridges: A:I.225 EDO.3: 5 residues within 4Å: Chain A: Q.54, N.83, L.84, N.85, L.99 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.84, A:N.85, A:N.85 Water bridges: A:N.85, A:L.99 EDO.4: 6 residues within 4Å: Chain A: L.49, Q.50, G.51, T.53, V.95, L.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.53 Water bridges: A:G.51 EDO.5: 5 residues within 4Å: Chain A: Q.70, W.77, F.156, Q.157, F.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.70 Water bridges: A:F.158 EDO.7: 6 residues within 4Å: Chain A: Q.236, Q.240 Chain B: P.7, L.9, E.233, H.237 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.237 Water bridges: A:Q.236 EDO.8: 5 residues within 4Å: Chain B: Q.70, W.77, F.156, Q.157, F.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.70 Water bridges: B:F.158 EDO.9: 6 residues within 4Å: Chain B: L.49, Q.50, G.51, T.53, V.95, L.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.53 Water bridges: B:G.51 EDO.10: 5 residues within 4Å: Chain B: Q.54, N.83, L.84, N.85, L.99 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.84, B:N.85, B:N.85 Water bridges: B:T.87, B:L.99

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: S.5, L.6, I.8, R.293, F.294 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain B: S.5, L.6, I.8, R.293, F.294 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Singh, B.K. et al., Structural Evolution of the Emerging 2014-2015 GII.17 Noroviruses. J.Virol. (2015)

Release Date

2016-01-13

Peptides

Capsid protein VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein VP1