SMTL ID : 5iyq.1

Protruding domain of GII.4 human norovirus CHDC2094 in complex with HBGA type B (triglycan)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-dimer

Ligands

2 x GLA- FUC- GLA: alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose(Non-functional Binders)

GLA-FUC-GLA.1: 10 residues within 4Å: Chain A: S.119, T.120, R.121, A.122, H.123, D.150 Chain B: K.124, S.217, G.218, Y.219 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.120, A:R.121, A:R.121, A:D.150, B:G.218, B:K.124 Water bridges: A:D.150, A:D.150, A:Q.152, A:Q.152, A:A.122, A:A.122, A:H.123, A:H.123, A:H.123, A:D.150 Hydrophobic interactions: B:Y.219 GLA-FUC-GLA.2: 10 residues within 4Å: Chain A: K.124, S.217, G.218, Y.219 Chain B: S.119, T.120, R.121, A.122, H.123, D.150 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:Y.219 Hydrogen bonds: A:G.218, B:T.120, B:R.121, B:R.121, B:D.150, A:K.124 Water bridges: B:D.150, B:Q.152, B:Q.152, B:A.122, B:A.122, B:H.123, B:H.123, B:H.123, B:D.150, B:D.150, B:D.150, B:D.150

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

EDO.3: 5 residues within 4Å: Chain A: L.48, Q.53, L.54, L.97 Chain B: E.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.12 EDO.4: 8 residues within 4Å: Chain A: T.9, V.10, E.11, F.252, I.284, P.285, P.286, G.288 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.10, A:E.11, A:E.11, A:G.288 Water bridges: A:T.9, A:T.9 EDO.5: 10 residues within 4Å: Chain A: S.14, S.55, A.56, Q.230, E.231 Chain B: S.14, S.55, A.56, Q.230, E.231 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.56, A:A.56 Water bridges: B:E.231 EDO.6: 3 residues within 4Å: Chain A: H.276, Y.280, M.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.305 Water bridges: A:Y.280 EDO.7: 6 residues within 4Å: Chain A: L.48, L.49, G.50, T.52, I.93, L.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.52 Water bridges: A:L.48, A:G.50 EDO.8: 7 residues within 4Å: Chain A: Q.107, K.124, A.125, T.126, T.144, T.145, D.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.107, A:T.126, A:T.144 Water bridges: A:K.124 EDO.9: 8 residues within 4Å: Chain A: W.84, T.111, Q.112, N.156, T.157, K.158 Chain B: P.214, G.215 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.111, A:T.111 Water bridges: A:T.113, A:T.113, A:T.113, B:G.215, B:G.215 EDO.10: 6 residues within 4Å: Chain B: L.48, L.49, G.50, T.52, I.93, L.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.52 Water bridges: B:L.48, B:G.50 EDO.11: 2 residues within 4Å: Chain B: N.297, F.299 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.297, B:N.297 EDO.12: 9 residues within 4Å: Chain B: Y.26, G.28, P.29, F.33, Q.177, W.178, F.208, R.210, D.225 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.29, B:W.178, B:R.210, B:D.225, B:D.225 Water bridges: B:Q.177 EDO.13: 7 residues within 4Å: Chain B: Q.107, K.124, A.125, T.126, T.144, T.145, D.146 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.107, B:T.144 Water bridges: B:K.124 EDO.14: 3 residues within 4Å: Chain B: V.132, H.133, T.135 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.132

1 x FLC: CITRATE ANION(Non-functional Binders)

FLC.15: 3 residues within 4Å: Chain B: S.131, V.132, H.133 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.132 Hydrogen bonds: B:V.132 Water bridges: B:H.133, B:Q.142 Salt bridges: B:H.133, B:H.133

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Singh, B.K. et al., Four decades of structural evolution of GII.4 norovirus. To be published

Release Date

2017-04-05

Peptides

Protruding domain of GII.4 norovirus CHDC2094 capsid: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protruding domain of GII.4 norovirus CHDC2094 capsid