SMTL ID : 4f5c.1 (1 other biounit)

Crystal structure of the spike receptor binding domain of a porcine respiratory coronavirus in complex with the pig aminopeptidase N ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: N.407, D.410, M.574, V.603, N.604, V.634, I.635 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain B: G.296, L.297, G.298, N.314, F.351 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.351

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.365, E.366, H.369, E.388 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.365, A:H.369, A:E.388, A:E.388, H2O.1

9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 3 residues within 4Å: Chain A: N.106, G.161, E.162 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.162 Hydrogen bonds: A:N.106 NAG.5: 8 residues within 4Å: Chain A: S.62, Y.63, N.64, I.86, R.88, N.211, T.248 Ligands: NAG.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.62, A:S.62, A:R.88, A:R.88, A:N.211, A:T.248 NAG.6: 1 residues within 4Å: Chain A: N.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.219 NAG.7: 2 residues within 4Å: Chain A: Y.293, N.296 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.293 Hydrogen bonds: A:N.296 NAG.8: 1 residues within 4Å: Chain A: N.310 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.310 NAG.9: 3 residues within 4Å: Chain A: L.59, A.205, N.488 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.59 Hydrogen bonds: A:N.488, A:N.488 NAG.10: 3 residues within 4Å: Chain A: N.628, S.630, V.631 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.628 NAG.11: 6 residues within 4Å: Chain A: N.64, I.86, E.154, K.229, E.245 Ligands: NAG.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.86 Hydrogen bonds: A:N.64, A:K.229, A:E.245 NAG.12: 4 residues within 4Å: Chain A: N.718 Chain B: Y.304, Q.306, I.308 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.306 Hydrogen bonds: B:Q.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reguera, J. et al., Structural bases of coronavirus attachment to host aminopeptidase N and its inhibition by neutralizing antibodies. Plos Pathog. (2012)

Release Date

2012-08-22

Peptides

Aminopeptidase N: A
PRCV spike protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Aminopeptidase N

PRCV spike protein

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