SMTL ID : 4opo.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

NAG-GAL-FUC-FUC.1: 12 residues within 4Å: Chain A: S.122, T.123, R.124, H.126, D.153 Chain B: Q.169, D.170, G.171, S.172, S.221, G.222, Y.223 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.171, B:S.172, B:S.172, B:S.221, B:G.171 Water bridges: A:D.153, B:C.220, B:S.221, B:Y.223, B:Y.223 NAG-GAL-FUC-FUC.2: 12 residues within 4Å: Chain A: Q.169, D.170, G.171, S.172, S.221, G.222, Y.223 Chain B: S.122, T.123, R.124, H.126, D.153 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.170, A:G.171, A:S.221, A:S.221, A:G.171 Water bridges: A:D.170, A:S.172, A:C.220, B:D.153, B:D.153

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

ACT.3: 7 residues within 4Å: Chain A: L.265, F.266, H.284, L.286, V.287, I.288, M.309 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.286 Hydrogen bonds: A:V.287, A:V.287 Salt bridges: A:H.284 ACT.6: 6 residues within 4Å: Chain B: L.265, F.266, H.284, L.286, V.287, M.309 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.265 Hydrogen bonds: B:V.287 Water bridges: B:H.284 Salt bridges: B:H.284

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

EDO.4: 6 residues within 4Å: Chain A: T.46, D.48, V.50, A.247, K.272 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.272 Water bridges: A:K.272 EDO.5: 5 residues within 4Å: Chain A: T.46, L.52, K.272, S.273 Ligands: EDO.4 No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain B: L.51, L.52, G.53, T.55, I.96, L.100 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.55 Water bridges: B:G.53, B:G.53 EDO.8: 6 residues within 4Å: Chain A: E.14, E.15 Chain B: Q.56, L.57, S.58, L.85 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.57 EDO.9: 5 residues within 4Å: Chain B: V.37, Q.39, W.182, V.183, L.184 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.182, B:L.184 Water bridges: B:Q.39

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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