SMTL ID : 6gw2.1

GII.10 human norovirus protruding domain in complex with taurochenodeoxycholate (TCDCA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x TUD: TAUROCHENODEOXYCHOLIC ACID(Non-covalent)

TUD.1: 11 residues within 4Å: Chain A: H.74, R.75, G.76, H.78, Q.109, V.137, Y.141, P.143, S.155, T.156, W.157 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.137, A:V.137, A:W.157, A:W.157 Hydrogen bonds: A:R.75 Water bridges: A:Q.109 Salt bridges: A:H.183 TUD.5: 13 residues within 4Å: Chain B: D.72, H.74, R.75, G.76, H.78, Q.109, V.137, Y.141, S.142, P.143, S.155, T.156, W.157 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.137, B:V.137, B:W.157, B:W.157 Hydrogen bonds: B:Y.141 Water bridges: B:Q.109, B:Y.141

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

EDO.2: 7 residues within 4Å: Chain A: P.6, L.8, E.240, H.244 Chain B: Q.243, Q.247 Ligands: EDO.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.244 Water bridges: B:Q.247 EDO.3: 4 residues within 4Å: Chain A: L.48, Q.53, L.54 Chain B: E.12 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.12, B:E.12, A:L.54 Water bridges: A:Q.53 EDO.4: 3 residues within 4Å: Chain A: N.131, R.132 Chain B: G.227 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.132, A:R.132, B:G.227 EDO.6: 6 residues within 4Å: Chain A: Q.243, Q.247 Chain B: L.8, E.240, H.244 Ligands: EDO.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.243, A:Q.243 Hydrogen bonds: B:H.244 EDO.7: 4 residues within 4Å: Chain A: E.12 Chain B: L.48, Q.53, L.54 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.54, A:E.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kilic, T. et al., Structural Basis for Human Norovirus Capsid Binding to Bile Acids. J. Virol. (2019)

Release Date

2018-10-17

Peptides

Capsid protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein

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