SMTL ID : 8wlo.1

Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with hippopotamus ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

12 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: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.801 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: N.717, F.718, T.719, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.10: 4 residues within 4Å: Chain C: N.801, F.802, S.803, N.928 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: C.1082, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.13: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: G.339, N.343 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.709 Chain B: D.796 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.1074, F.1075, T.1076, N.1098 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.343 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.17, N.137 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: S.112, E.132, N.164, N.165 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.709, N.710 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.331, I.332 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: E.132, N.165 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.709, N.710 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.616, T.618, E.619 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.17, T.20, R.21, F.79 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.38: 2 residues within 4Å: Chain D: H.356, H.360 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.356, D:H.360

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, R. et al., Molecular basis of hippopotamus ACE2 binding to SARS-CoV-2. J.Virol. (2024)

Release Date

2024-03-27

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

Spike glycoprotein

Angiotensin-converting enzyme

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