SMTL ID : 2zl7.1

Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

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

GAL-FUC-NGA.1: 6 residues within 4Å: Chain B: D.103, H.105, W.151, S.153, P.154, S.156 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.156, B:S.156, B:D.103, B:H.105, B:H.105, B:S.153, B:S.153 Water bridges: B:N.138, B:N.138, B:S.156, B:S.156

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: T.123, T.124, P.125, F.128, N.170, G.172 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.123, H2O.14

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: P.10, L.12, Y.217, V.276, F.277 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:P.10, A:L.12, A:Y.217 MG.5: 5 residues within 4Å: Chain B: P.10, L.12, Y.217, V.276, F.277 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:P.10, B:L.12, B:Y.217

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

ACT.4: 6 residues within 4Å: Chain A: K.65, L.80, F.111, V.146 Chain B: L.24, P.25 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.80, A:V.146, B:P.25 Salt bridges: A:K.65 ACT.6: 6 residues within 4Å: Chain A: L.24, P.25 Chain B: K.65, L.80, F.111, V.146 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.80, B:V.146, A:P.25 Salt bridges: B:K.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, J.M. et al., Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-07-22

Peptides

58 kd capsid protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

58 kd capsid protein

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