SMTL ID : 2zl5.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: T.123, T.124, P.125, F.128, N.170, G.172 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.128, A:N.170, H2O.307 CA.7: 4 residues within 4Å: Chain B: T.47, L.48, D.49, P.253 No protein-ligand interaction detected (PLIP)

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

ACT.2: 5 residues within 4Å: Chain A: K.65, F.111, V.146 Chain B: L.24, P.25 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.25, A:V.146 Salt bridges: A:K.65 ACT.3: 6 residues within 4Å: Chain A: G.100, G.101, T.123, K.167, I.168, P.169 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.167 Hydrogen bonds: A:G.101, A:T.123 Water bridges: A:C.102, A:C.102, A:C.102, A:T.123, A:N.170 Salt bridges: A:K.167 ACT.6: 6 residues within 4Å: Chain B: G.100, G.101, T.123, K.167, I.168, P.169 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.101, B:T.123 Water bridges: B:C.102, B:C.102, B:C.102, B:T.123

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 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

Links

RCSB   PDBe   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