SMTL ID : 7cn9.1

Cryo-EM structure of SARS-CoV-2 Spike ectodomain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

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 C: A.693, E.1059, K.1060, N.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: N.704, L.909, N.912 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.912 NAG-NAG.5: 1 residues within 4Å: Chain B: N.704 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: S.698, N.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain A: N.704, N.912 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain A: N.152 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 1 residues within 4Å: Chain C: N.152 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 5 residues within 4Å: Chain A: N.318, I.319, Q.567, T.568, L.569 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.9: 2 residues within 4Å: Chain A: K.545 Chain B: N.269 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.12: 2 residues within 4Å: Chain A: N.788, S.790 No protein-ligand interaction detected (PLIP)

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

NAG.14: 2 residues within 4Å: Chain A: N.603, T.605 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.644 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: V.692, N.1061 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: C.1069, D.1071, N.1121 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: N.109, N.112, V.114, K.116, E.156 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.267, N.269, T.271 Chain C: K.545 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.318 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.590, T.591 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: D.601, V.602, N.603 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.644 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.696 Chain C: D.783 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.221 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.151, N.152 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.1121 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.696 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: V.643, N.644 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: T.294, N.590 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: Y.15, T.16, N.17, N.48 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: P.317, N.318, I.319 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y.M. et al., A Carbohydrate-Binding Protein from the Edible Lablab Beans Effectively Blocks the Infections of Influenza Viruses and SARS-CoV-2. Cell Rep (2020)

Release Date

2020-08-26

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein