SMTL ID : 6xm3.1

Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

17 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, S.446, N.447, K.449, E.452 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.704, L.909, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.788, S.790 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: A.693, E.1059, N.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1085, T.1087, 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: T.95, N.221 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.318, Q.567 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: G.326, F.329, N.330 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.704 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.1085, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.704, L.909, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.788, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: N.1085, T.1087, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 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.18: 3 residues within 4Å: Chain A: F.46, N.48, P.618 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.109, T.111 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.267, E.268, N.269 Chain C: K.545 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.318, Q.567 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: F.325, G.326, N.330 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.590, T.591 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.603 Chain B: I.831, R.834 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.644 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.696, G.1118 Chain B: D.783 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: E.119, N.152 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.48 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.267, E.268, N.269 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.644 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.696, I.1117 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.152 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.48 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.267, E.268, N.269 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.318, Q.567 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: G.326, N.330 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.644 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.696, I.1117 Ligand excluded by PLIP NAG.43: 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

2020-08-12

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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