SMTL ID : 6u7g.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.49 NAG-NAG.2: 6 residues within 4Å: Chain A: D.372, Q.535, L.563, N.564, V.594, I.595 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.327, H.331, E.350, A.353, Y.416 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.327, A:H.331, A:E.350, A:E.350, H2O.10

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

NAG.4: 7 residues within 4Å: Chain A: R.37, L.39, V.41, N.67, E.122, G.123, E.124 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.39 Hydrogen bonds: A:R.37, A:R.37, A:N.67 NAG.5: 10 residues within 4Å: Chain A: H.178, K.180, D.181, L.182, T.183, S.194, T.195, P.196, N.204 Chain B: P.26 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.180, A:S.194, A:N.204 NAG.6: 8 residues within 4Å: Chain A: D.254, Y.255, N.258, F.308, P.310, K.318 Chain B: N.116, L.117 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.255 Hydrogen bonds: A:N.258 NAG.7: 7 residues within 4Å: Chain A: E.575, R.579, P.614, T.616, L.617, N.620, W.900 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.614, A:L.617 Hydrogen bonds: A:E.575, A:R.579, A:R.579, A:T.616 NAG.8: 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 NAG.9: 4 residues within 4Å: Chain B: Y.17, N.19, N.38, T.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.38, B:T.40

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 protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Aminopeptidase N

Spike protein

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