SMTL ID : 4f5c.2 (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

1 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: 6 residues within 4Å: Chain B: G.296, L.297, G.298, S.313, 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.2: 5 residues within 4Å: Chain A: E.332, 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

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

NAG.3: 5 residues within 4Å: Chain A: I.80, N.106, Q.160, G.161, E.162 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.80 Hydrogen bonds: A:N.106, A:N.106 NAG.4: 7 residues within 4Å: Chain A: S.62, N.64, I.86, R.88, N.211, T.248 Ligands: NAG.8 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.5: 1 residues within 4Å: Chain A: N.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.219 NAG.6: 1 residues within 4Å: Chain A: N.268 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain A: N.628 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.628 NAG.8: 5 residues within 4Å: Chain A: N.64, I.86, E.154, E.245 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.86 Hydrogen bonds: A:E.245 NAG.9: 5 residues within 4Å: Chain A: N.718 Chain B: Y.304, Q.306, I.308, Q.410 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.306 Hydrogen bonds: B:Q.306 NAG.10: 4 residues within 4Å: Chain A: Y.293, N.296, F.346, K.356 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.293, A:F.346 Hydrogen bonds: A:N.296, A:K.356 NAG.11: 2 residues within 4Å: Chain A: N.310, S.312 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.310 NAG.12: 5 residues within 4Å: Chain A: L.59, A.205, F.484, Q.487, N.488 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.59 Hydrogen bonds: A:N.488, A:N.488 NAG.13: 2 residues within 4Å: Chain A: M.574, N.604 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.604

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
B

B
F

Aminopeptidase N

PRCV spike protein

Related Entries With Identical Sequence