SMTL ID : 7vpq.3 (2 other biounits)

Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 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: 5 residues within 4Å: Chain A: D.372, Q.535, L.563, N.564, I.595 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: S.23, Y.24, R.25, T.47, R.49, N.173, T.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.49, A:R.49

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: E.294, H.327, E.328, H.331, E.350, Y.416 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.327, A:H.331, A:E.350, A:E.350

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

NAG.4: 3 residues within 4Å: Chain A: T.616, N.620, L.623 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.616, A:T.616, A:N.620 NAG.5: 3 residues within 4Å: Chain A: N.723, N.757, T.759 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.757 NAG.6: 4 residues within 4Å: Chain A: K.231, N.258, P.262 Chain B: D.18 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.18, A:N.258 Hydrophobic interactions: A:P.262 NAG.7: 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.8: 6 residues within 4Å: Chain A: R.37, L.39, V.41, N.67, G.123, E.124 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.41 Hydrogen bonds: A:R.37, A:R.37 NAG.10: 4 residues within 4Å: Chain B: Q.10, N.12, T.28, N.47 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.28 Hydrogen bonds: B:T.28

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: S.316, E.319, L.373, N.377, Y.690 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.316, A:N.377, A:N.377, A:Y.631

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ji, W. et al., Structures of a deltacoronavirus spike protein bound to porcine and human receptors. Nat Commun (2022)

Release Date

2022-03-16

Peptides

Aminopeptidase N: A
Spike protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Aminopeptidase N

Spike protein

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