SMTL ID : 7kni.1

Cryo-EM structure of Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 5.5

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

6 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: T.716, N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.717, L.922, N.925, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.925 NAG-NAG.4: 4 residues within 4Å: Chain D: K.398, S.402, D.525, N.528 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain E: K.398, S.402, D.525, N.528 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain F: K.398, S.402, D.525, N.528 No protein-ligand interaction detected (PLIP)

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

NAG.7: 6 residues within 4Å: Chain A: P.330, N.331, I.332, T.333, Q.580, L.582 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.709 Chain B: I.794, D.796 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: A.706, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.234, T.236 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: S.112, E.132, N.164, N.165 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: E.309, N.603 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain B: N.331, I.332, P.579, Q.580, T.581 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: K.558 Chain B: E.281, N.282 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.801, S.803 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.709 Chain C: I.794 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.234, T.236 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: S.112, E.132, N.164, N.165 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain B: F.338, F.342, N.343, S.371, S.373 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: S.711, N.1074, F.1075, T.1076 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain C: N.331, P.579, Q.580, T.581, L.582 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.801, S.803 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: D.796 Chain C: N.709 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.234, T.236 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: S.112, E.132, N.164, N.165 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain C: F.338, F.342, N.343, S.371, S.373 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: E.309, N.603 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain D: E.294, N.304, M.305 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: D.413, N.414 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain D: Q.63, N.85, A.175, H.177 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain D: K.8, N.72, T.74 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain D: N.35, I.36, T.37, V.321 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain E: E.294, N.304, M.305 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain E: D.413, N.414 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: Q.63, N.85, A.175 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: 2 residues within 4Å: Chain F: N.304, M.305 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain F: D.413, N.414 Ligand excluded by PLIP NAG.60: 5 residues within 4Å: Chain F: Q.63, Q.83, N.85, A.175, H.177 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain F: N.72, T.74 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain F: N.35, I.36, T.37, V.321 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

2020-12-16

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme 2: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

E
D

F
E

Spike glycoprotein

Angiotensin-converting enzyme 2

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