SMTL ID : 5iyp.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

homo-dimer

Ligands

2 x GLA- FUC- A2G: alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose

GLA-FUC-A2G.1: 8 residues within 4Å: Chain A: S.120, T.121, R.122, H.124, D.151 Chain B: S.218, G.219, Y.220 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Water bridges: A:T.148, A:N.150, A:D.151, B:K.125, A:Q.153, A:Q.153, A:Q.153 Hydrogen bonds: A:T.121, A:R.122, A:R.122, A:D.151, B:G.219 Hydrophobic interactions: B:Y.220 GLA-FUC-A2G.2: 10 residues within 4Å: Chain A: K.125, S.218, G.219, Y.220 Chain B: S.120, T.121, R.122, A.123, H.124, D.151 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:K.125, B:T.121, B:R.122, B:R.122, B:D.151, A:G.219 Water bridges: B:A.123, B:H.124, B:H.124, B:H.124, B:T.148, B:T.148, B:D.151, B:D.151, B:Q.153, A:D.168, A:D.168, A:D.168, A:S.218 Hydrophobic interactions: A:Y.220

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

EDO.3: 3 residues within 4Å: Chain A: H.277, Y.281, M.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.306 EDO.4: 8 residues within 4Å: Chain A: T.10, V.11, E.12, F.253, I.285, P.286, P.287, G.289 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.11, A:E.12, A:G.289 Water bridges: A:T.10, A:T.10 EDO.5: 6 residues within 4Å: Chain A: L.49, L.50, G.51, T.53, I.94, L.98 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.53 Water bridges: A:L.49, A:G.51, A:G.51 EDO.6: 6 residues within 4Å: Chain A: L.49, Q.54, L.55, L.98, Y.238 Chain B: E.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.13 EDO.7: 10 residues within 4Å: Chain A: S.15, S.56, A.57, Q.231, E.232 Chain B: S.15, S.56, A.57, Q.231, E.232 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.57, B:A.57 Water bridges: A:E.232 EDO.8: 7 residues within 4Å: Chain A: L.262, F.263, Y.281, L.283, V.284, I.285, M.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.284 EDO.10: 6 residues within 4Å: Chain B: L.49, L.50, G.51, T.53, I.94, L.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.53 Water bridges: B:L.49, B:G.51

1 x FLC: CITRATE ANION(Non-covalent)

FLC.9: 3 residues within 4Å: Chain B: S.132, V.133, H.134 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.133 Hydrogen bonds: B:V.133 Water bridges: B:H.134, B:Q.143 Salt bridges: B:H.134, B:H.134

Links

RCSB   PDBe   PDBe-KB   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

VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VP1

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