SMTL ID : 7kmz.1

Cryo-EM structure of double ACE2-bound SARS-CoV-2 trimer Spike at pH 7.4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

4 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: 3 residues within 4Å: Chain A: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: F.338, G.339, N.343, S.371 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: S.112, E.132, N.164, N.165 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.331, I.332, Q.580 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.801 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: A.706, N.1074 Chain D: Q.895 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.234, T.236 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: S.112, Q.115, E.132, N.164, N.165 Ligand excluded by PLIP NAG.30: 7 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, V.367, S.371, S.373 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: E.309, N.603 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: D.525, N.528 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: E.294, N.304, M.305, Q.307 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: D.413, N.414 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain C: Q.63, N.85, V.89, A.175, N.176 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.72 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.35, T.37, Q.322 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain D: N.331, Q.580 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain D: N.1134 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: K.558 Chain D: N.280, N.282 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain D: N.657 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain D: N.616 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain D: N.801, S.803 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain A: D.796 Chain D: N.709, G.1131 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain D: N.1074 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain D: Y.28, N.61 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: G.232, N.234 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain D: N.165 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain D: F.338, G.339, F.342, N.343, V.367 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain E: K.398, S.402, D.525, N.528 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain E: N.304, Q.307 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain E: D.413, N.414, E.415 Ligand excluded by PLIP NAG.55: 6 residues within 4Å: Chain E: N.85, S.88, V.89, A.175, N.176, H.177 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain E: N.72, L.73 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain E: N.31, N.35, T.37 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains. Cell Host Microbe (2020)

Release Date

2020-12-09

Peptides

Spike glycoprotein: ABD
Angiotensin-converting enzyme 2: CE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

D
B

C
E

E
D

Spike glycoprotein

Angiotensin-converting enzyme 2

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