SMTL ID : 7vs9.1

Crystal structure of P domain from norovirus GI.9 capsid protein in complex with Lewis x antigen.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

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

NDG-FUC-GAL.1: 10 residues within 4Å: Chain A: D.107, H.109, W.167, S.169, N.170, R.171, A.172, V.217 Chain B: A.122, N.123 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.167, A:V.217 Hydrogen bonds: A:N.170, A:N.170, B:N.123, A:N.130, A:S.169, A:S.169, B:N.123 Water bridges: A:R.175, A:N.173 NDG-FUC-GAL.2: 9 residues within 4Å: Chain A: A.122, N.123 Chain B: D.107, H.109, W.167, S.169, N.170, A.172, V.217 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.167, B:V.217 Hydrogen bonds: B:N.170, B:N.170, A:N.123, B:D.107, B:H.109, B:S.169, B:S.169, A:N.123 Water bridges: B:R.175, B:N.173

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: S.94 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:S.94, H2O.1, H2O.4, H2O.6, H2O.7, H2O.9 MG.13: 1 residues within 4Å: Chain B: S.94 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:S.94, H2O.12, H2O.15, H2O.15, H2O.17, H2O.19

16 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain A: R.245 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: T.3, K.4, Q.5 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: T.3, K.4, P.243 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: S.7, V.8, N.10, F.295 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: M.51, T.56, V.57, L.98 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: T.116, P.117, S.118 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: G.246 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: T.282, Q.285, S.286 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: S.300, Y.303 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: S.7, V.8, N.10, F.295 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: R.245 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: M.51, T.56, V.57 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: T.116, P.117, S.118 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: N.183, Y.184, G.185 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: T.282, Q.285, S.286 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: S.300, Y.303 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kimura-Someya, T. et al., Lewis fucose is a key moiety for the recognition of histo-blood group antigens by GI.9 norovirus, as revealed by structural analysis. Febs Open Bio (2022)

Release Date

2022-08-31

Peptides

VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VP1

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