SMTL ID : 4wzl.1

Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type Lea (triglycan)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x NDG- GAL- FUC: beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-functional Binders)

NDG-GAL-FUC.1: 8 residues within 4Å: Chain A: S.121, T.122, R.123, D.152 Chain B: G.170, S.220, G.221, Y.222 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.122, A:R.123, A:R.123, A:D.152, B:S.220, B:G.221, B:Y.222 Water bridges: A:D.152, A:S.121, A:D.152, B:C.219 Hydrophobic interactions: B:Y.222 NDG-GAL-FUC.2: 8 residues within 4Å: Chain A: G.170, S.220, G.221, Y.222 Chain B: S.121, T.122, R.123, D.152 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.122, B:R.123, B:R.123, B:D.152, A:S.220, A:G.221, A:Y.222 Water bridges: B:D.152, B:E.154, B:S.121, A:C.219 Hydrophobic interactions: A:Y.222

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

EDO.3: 8 residues within 4Å: Chain A: F.28, S.32, F.35, Q.180, W.181, F.211, R.213, D.228 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.181, A:R.213, A:D.228, A:D.228 Water bridges: A:P.31, A:Q.180, A:Q.282 EDO.4: 6 residues within 4Å: Chain A: L.50, L.51, G.52, T.54, I.95, L.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.54 Water bridges: A:G.52, A:E.94 EDO.5: 8 residues within 4Å: Chain A: T.63, F.64, R.65, L.81, A.82, S.83, L.84, P.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.63, A:R.65, A:R.65 EDO.6: 5 residues within 4Å: Chain A: V.36, Q.38, W.181, V.182, L.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.38, A:W.181, A:L.183 EDO.9: 8 residues within 4Å: Chain B: F.28, S.32, F.35, Q.180, W.181, F.211, R.213, D.228 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.181, B:R.213, B:D.228 Water bridges: B:P.31, B:Q.180, B:R.213, B:Q.282 EDO.10: 8 residues within 4Å: Chain B: T.63, F.64, R.65, L.81, A.82, S.83, L.84, P.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.63, B:R.65, B:R.65 EDO.11: 6 residues within 4Å: Chain B: L.50, L.51, G.52, T.54, I.95, L.99 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.54 Water bridges: B:L.50, B:G.52, B:E.94 EDO.12: 5 residues within 4Å: Chain B: V.36, Q.38, W.181, V.182, L.183 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.38, B:W.181, B:L.183 EDO.13: 7 residues within 4Å: Chain B: V.105, G.132, V.182, L.183, P.184, S.185, R.189 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.132, B:S.185, B:S.185 Water bridges: B:L.183

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 6 residues within 4Å: Chain A: Q.55, L.56, S.57, N.60 Chain B: E.13, E.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.55, A:L.56 ACT.8: 6 residues within 4Å: Chain A: L.264, H.283, L.285, V.286, I.287, M.308 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.264 Hydrogen bonds: A:V.286 Salt bridges: A:H.283 ACT.14: 6 residues within 4Å: Chain A: E.13, E.14 Chain B: Q.55, L.56, S.57, N.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.56 ACT.15: 5 residues within 4Å: Chain B: L.264, H.283, L.285, V.286, M.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.286 Salt bridges: B:H.283

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Singh, B.K. et al., Human noroviruses' fondness for histo-blood group antigens. J.Virol. (2015)

Release Date

2014-12-17

Peptides

VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VP1

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