SMTL ID : 7u0l.1

Crystal structure of the CCoV-HuPn-2018 RBD (domain B) in complex with canine APN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- GAL- MAN: alpha-D-mannopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-GAL-MAN.1: 7 residues within 4Å: Chain A: N.22, T.44, R.76, N.170, R.188, E.204 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 2 residues within 4Å: Chain A: D.369, N.563 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 7 residues within 4Å: Chain B: L.15, G.16, L.30, S.31, N.32, K.61, F.69 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.30

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.3: 6 residues within 4Å: Chain A: Q.676, N.677, D.708 Chain B: Y.22, Q.24, I.26 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.24 Hydrophobic interactions: A:D.708

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 2 residues within 4Å: Chain A: Q.753, N.756 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 6 residues within 4Å: Chain A: H.175, S.177, L.179, S.191, P.193, N.201 No protein-ligand interaction detected (PLIP)

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.5: 5 residues within 4Å: Chain A: N.34, T.38, N.64, G.120, E.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.34 NAG-NAG.9: 6 residues within 4Å: Chain A: Q.574, K.578, P.613, T.615, L.616, N.619 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.6: 11 residues within 4Å: Chain A: S.20, N.22, T.44, R.46, G.79, G.80, N.170, R.188, T.207 Ligands: NAG-NAG-GAL-MAN.1, NAG-NAG-GAL-MAN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.46

2 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.8: 5 residues within 4Å: Chain A: S.438, T.442, W.459, G.462, N.463 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.442 NAG-NAG-BMA-MAN-FUC.11: 4 residues within 4Å: Chain B: T.8, N.10, Y.55, H.57 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 4 residues within 4Å: Chain A: E.291, H.324, H.328, E.347 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.324, A:H.328, A:E.347, A:E.347

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

NAG.13: 2 residues within 4Å: Chain A: M.185, N.275 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.275 NAG.14: 2 residues within 4Å: Chain A: N.510, T.512 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tortorici, M.A. et al., Structure, receptor recognition, and antigenicity of the human coronavirus CCoV-HuPn-2018 spike glycoprotein. Cell (2022)

Release Date

2022-08-24

Peptides

Aminopeptidase N: A
Spike glycoprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminopeptidase N

Spike glycoprotein