SMTL ID : 7vpp.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-2-1-mer

Ligands

9 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: N.25, I.47, E.115, K.190 Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 9 residues within 4Å: Chain A: S.23, Y.24, N.25, R.49, N.172, K.190, T.209 Ligands: NAG-NAG.1, NAG-NAG.1 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: A.166, F.445, Q.448, N.449 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: K.143, N.180, E.224 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.143 NAG-NAG.5: 5 residues within 4Å: Chain A: I.41, N.67, Q.121, G.122, E.123 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: V.141, K.143, N.180, E.224 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain C: S.23, Y.24, N.25, R.49, N.172, T.209 Ligands: NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: A.166, F.445, Q.448, N.449 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: D.37, L.39, N.67 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.9: 4 residues within 4Å: Chain C: D.371, I.564, N.565, I.596 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.11: 5 residues within 4Å: Chain A: E.293, H.326, H.330, E.349, Y.415 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.326, A:H.330, A:E.349, A:E.349, H2O.1 ZN.18: 5 residues within 4Å: Chain C: E.293, H.326, H.330, E.349, Y.415 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.326, C:H.330, C:E.349, C:E.349, H2O.2

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 7 residues within 4Å: Chain A: A.289, G.290, A.291, V.323, H.326, E.327, Y.415 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.290, A:A.291, A:H.326 GOL.13: 2 residues within 4Å: Chain A: A.383, Q.843 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.843 GOL.14: 4 residues within 4Å: Chain A: T.27, R.29, K.43, G.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29, A:G.44 GOL.19: 4 residues within 4Å: Chain C: G.290, A.291, H.326, E.327 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.290, C:A.291, C:E.327 Water bridges: C:Y.415 GOL.20: 4 residues within 4Å: Chain C: P.375, G.376, Y.632, Q.636 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.375, C:Q.636

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

NAG.15: 4 residues within 4Å: Chain A: D.371, M.535, I.564, N.565 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.564 Hydrogen bonds: A:D.371, A:N.565 NAG.16: 4 residues within 4Å: Chain A: E.230, N.257, P.261 Chain B: F.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.261 NAG.17: 3 residues within 4Å: Chain B: Q.10, N.12, N.47 No protein-ligand interaction detected (PLIP) NAG.21: 5 residues within 4Å: Chain C: N.25, I.47, E.115, K.190 Ligands: NAG-NAG.7 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.47 Hydrogen bonds: C:N.25, C:E.206 NAG.22: 3 residues within 4Å: Chain C: M.253, Y.254, N.257 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.254 Hydrogen bonds: C:N.257

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: AC
Spike protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

Aminopeptidase

Spike protein

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