SMTL ID : 7knb.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

5 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: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: F.342, N.343, V.367 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: Y.489 Chain B: F.338, G.339, F.342, N.343 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.489 NAG-NAG.5: 3 residues within 4Å: Chain C: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP)

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

NAG.6: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: S.112, E.132, N.164, N.165 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: R.328, N.331, S.530, Q.580 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.280, N.282 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.801, S.803 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 C: Q.895 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.28: 7 residues within 4Å: Chain A: K.462, P.463, F.464, E.465, R.466 Chain B: I.233, N.234 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: K.113, E.132, N.164, N.165 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.331, I.332, Q.580 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.801, Q.804 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: Q.895 Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: T.114, N.234, T.236 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: S.112, E.132, N.164, N.165 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: F.338, N.343, V.367 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain D: N.528 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain D: N.304, Q.307 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain D: D.413, N.414, E.415 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain D: Q.63, N.85, V.89, N.176 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain D: K.8, N.72, T.74 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain D: N.35, I.36, T.37, Q.322 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: ABC
Angiotensin-converting enzyme 2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
D

Spike glycoprotein

Angiotensin-converting enzyme 2

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