SMTL ID : 4oox.1

Crystal structure of P domain from norovirus strain Saga4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 7 residues within 4Å: Chain A: Q.55, L.56, S.57, N.60, L.84 Chain B: E.13, E.14 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.13, A:L.56, A:S.57 ACT.2: 5 residues within 4Å: Chain A: L.264, H.283, L.285, V.286, M.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.286 Salt bridges: A:H.283 ACT.11: 7 residues within 4Å: Chain A: E.13, E.14 Chain B: Q.55, L.56, S.57, N.60, L.84 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.13, B:L.56, B:S.57 ACT.12: 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

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

EDO.3: 6 residues within 4Å: Chain A: L.50, L.51, G.52, T.54, I.95, L.99 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: V.36, Q.38, W.181, V.182, L.183 Ligand excluded by PLIP EDO.5: 9 residues within 4Å: Chain A: F.28, S.32, F.35, Q.180, W.181, F.211, R.213, D.228, Q.282 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: T.63, F.64, R.65, L.81, A.82, S.83, L.84, P.98 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: N.76, V.129, Y.130, S.133, Q.144, F.145, S.146 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: S.133, R.189 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: K.3, Q.241, E.242 Chain B: I.9 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: V.105, G.132, V.182, L.183, P.184, S.185, R.189 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: L.50, L.51, G.52, T.54, I.95, L.99 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: V.36, Q.38, W.181, V.182, L.183 Ligand excluded by PLIP EDO.15: 9 residues within 4Å: Chain B: F.28, S.32, F.35, Q.180, W.181, F.211, R.213, D.228, Q.282 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain B: T.63, F.64, R.65, L.81, A.82, S.83, L.84, P.98 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain B: N.76, V.129, Y.130, S.133, Q.144, F.145, S.146 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain B: S.133, R.189 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: I.9 Chain B: K.3, Q.241, E.242 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: V.105, G.132, V.182, L.183, P.184, S.185, R.189 Ligand excluded by PLIP

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
A

VP1

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