SMTL ID : 6u7f.1 (1 other biounit)

HCoV-229E RBD Class IV in complex with human APN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 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: S.23, Y.24, R.25, T.47, R.49, N.173, T.210 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: D.372, Q.535, N.564, I.595 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.327, H.331, E.350, Y.416 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.327, A:H.331, A:E.350, H2O.5

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

NAG.4: 5 residues within 4Å: Chain A: R.37, L.39, N.67, G.123, E.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.37, A:R.37 NAG.5: 5 residues within 4Å: Chain A: K.180, L.182, S.194, P.196, N.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.180, A:S.194, A:N.204 NAG.6: 4 residues within 4Å: Chain A: Y.255, N.258, P.310 Chain B: N.116 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.255, A:P.310 Hydrogen bonds: A:N.258 NAG.7: 6 residues within 4Å: Chain A: Q.437, S.441, H.459, E.462, A.463, N.466 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.462 Hydrogen bonds: A:Q.437, A:E.462, A:E.462, A:E.462, A:N.466 NAG.8: 3 residues within 4Å: Chain A: T.616, L.617, N.620 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.616, A:N.620 NAG.9: 3 residues within 4Å: Chain A: R.673, N.674, N.678 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.673, A:N.674 NAG.10: 3 residues within 4Å: Chain B: Y.17, N.38, T.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.38, B:T.40 NAG.11: 3 residues within 4Å: Chain B: N.45, T.47, K.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Z. et al., The human coronavirus HCoV-229E S-protein structure and receptor binding. Elife (2019)

Release Date

2019-11-13

Peptides

Aminopeptidase N: A
Spike glycoprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Aminopeptidase N

Spike glycoprotein

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