SMTL ID : 6xm5.1

Structure of SARS-CoV-2 spike at pH 5.5, all RBDs down

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

16 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: 8 residues within 4Å: Chain A: T.95, N.221, T.223 Chain C: R.444, K.445, S.446, N.447, E.452 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.445 NAG-NAG.2: 3 residues within 4Å: Chain A: N.704, L.909, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: A.693, N.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.1085, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.221, T.223 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.318 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.704, L.909, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: N.1085, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain C: N.704, L.909 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.1085, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.1121 No protein-ligand interaction detected (PLIP)

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

NAG.17: 3 residues within 4Å: Chain A: Y.15, N.48, P.618 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.109 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.267, E.268, N.269 Chain C: K.545 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.318 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.330 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.603, T.605 Chain B: I.831, R.834 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.644 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.696, G.1118 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.151, N.152 Chain C: Y.338 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.269 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.644 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.696, G.1118 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.152 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: Y.15, N.48, P.618, R.621 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: K.545 Chain C: E.268, N.269 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.318, Q.567 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: F.325, G.326, F.329, N.330 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: H.642, N.644 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.696 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: A.693, E.1059, N.1061 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

2020-07-29

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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