SMTL ID : 3q6r.1

Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with disordered HBGA type Lex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: G.16, P.26, I.27, D.28 Chain B: L.60, N.92 Ligand excluded by PLIP EDO.2: 6 residues within 4Å: Chain A: P.11, L.13, E.245, H.249 Chain B: Q.248, Q.252 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: F.189, Q.191, R.224, P.236, A.237 Ligands: EDO.4 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: Y.31, N.33, E.36, Q.191, W.192, R.224, D.239 Ligands: EDO.3 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: L.60, T.62, G.63, A.66, L.91, K.174 Chain B: P.26 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: Q.58, N.90, L.91, N.92, L.106 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: P.98, T.99, E.100, D.101, K.153, M.205, N.206 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: L.53, Q.58, L.59 Chain B: E.17 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: P.24, P.61 Chain B: P.24, P.61, T.62 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: H.139, E.140, W.162 Chain B: E.140, K.230 Ligands: IMD.23 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: E.17 Chain B: L.53, L.59, L.106, Y.251 Ligands: EDO.17 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: R.80, G.81, V.142, S.160, T.161, W.162 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: G.232, Y.233 Chain B: A.135, N.136 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain A: P.26 Chain B: L.60, T.62, G.63, A.66, R.68, L.91, K.174 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: Q.58, N.90, L.91, N.92, L.106 Ligands: EDO.11 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: Q.248, Q.252 Chain B: P.11, L.13, E.245, H.249 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: F.226, I.227, P.228 Chain B: R.68, R.122 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: V.142, S.160, T.161, W.162 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain A: E.140, K.230 Chain B: H.139, E.140, W.162, E.163 Ligands: IMD.15, IMD.23 Ligand excluded by PLIP

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.14: 6 residues within 4Å: Chain A: L.53, Q.54, G.55, T.57, V.102, L.106 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.53 IMD.15: 5 residues within 4Å: Chain A: E.140, W.162, K.230 Chain B: H.139 Ligands: EDO.21 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.139, A:K.230 IMD.22: 5 residues within 4Å: Chain B: L.53, Q.54, G.55, T.57, L.106 No protein-ligand interaction detected (PLIP) IMD.23: 6 residues within 4Å: Chain A: H.139 Chain B: E.140, W.162, K.230 Ligands: EDO.10, EDO.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.230 pi-Stacking: B:W.162

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Hansman, G.S. et al., Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability. J.Virol. (2011)

Release Date

2011-05-11

Peptides

Capsid protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein

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