SMTL ID : 7kms.1

Cryo-EM structure of triple ACE2-bound SARS-CoV-2 trimer spike at pH 7.4

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

8 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: 4 residues within 4Å: Chain A: K.398, S.402, D.525, N.528 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain B: N.1134 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: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain D: D.1127, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain E: K.398, S.402, N.528 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: E.294, N.304, M.305 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: D.413, N.414 Ligand excluded by PLIP NAG.11: 5 residues within 4Å: Chain A: Q.63, N.85, V.89, A.175, N.176 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.72, L.73, T.74 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.35, I.36, T.37, V.321 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.280, N.282 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.801, S.803 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: A.706, N.1074 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: I.233, N.234 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: F.338, F.342, N.343 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.331 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.801 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: I.233, N.234 Chain D: H.519 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain D: N.331, Q.580 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain D: N.280, N.282 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain D: N.657 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain D: N.616, T.618 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain D: N.801 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain D: N.709, G.1131 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain D: A.706, N.1074 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: Y.28, N.61 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: I.233, N.234 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain D: N.603, T.604 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain D: N.165 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain D: G.339, F.342, N.343 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain E: E.294, N.304, M.305, Q.307 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain E: D.413, N.414 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain E: Q.63, N.85, A.175, N.176 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain E: N.72, T.74 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain E: N.35, I.36, T.37 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain F: K.398, S.402, D.525, N.528 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain F: E.294, N.304, M.305, Q.307 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain F: D.413, N.414 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain F: Q.63, N.85, V.89, A.175 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain F: N.72, L.73, T.74 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain F: N.35, I.36, 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

Angiotensin-converting enzyme 2: AEF
Spike glycoprotein: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

E
D

F
E

B
A

C
C

D
B

Angiotensin-converting enzyme 2

Spike glycoprotein

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