SMTL ID : 6x6p.1

Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 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: 2 residues within 4Å: Chain A: N.703, Q.1057 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.787, S.789, Q.790 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.1084, H.1087, F.1089 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1120 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.703, Q.1057 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.787, S.789, Q.790 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.1084, H.1087, F.1089 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1120 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: N.703, Q.1057 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.787, S.789, Q.790 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.1084, H.1087, F.1089 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1120 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: Y.14, N.47 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: T.94, N.220, T.222 Chain C: K.448 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.266, E.267, N.268 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: P.316, N.317, P.565, Q.566 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: F.324, G.325, F.328, N.329 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.589 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.602, T.604 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: H.641, N.643 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.695, G.1117 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: A.692, E.1058, N.1060 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.150, N.151 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: Y.14, N.47 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: K.448 Chain B: T.94, N.220, T.222 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.266, E.267, N.268 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: P.316, N.317, P.565, Q.566 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: F.324, G.325, F.328, N.329 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.589 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.602, T.604 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: H.641, N.643 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.695, G.1117 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: A.692, E.1058, N.1060 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.150, N.151 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: Y.14, N.47 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: K.448 Chain C: T.94, N.220, T.222 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.266, E.267, N.268 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: P.316, N.317, P.565, Q.566 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: F.324, G.325, F.328, N.329 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.589 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.602, T.604 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: H.641, N.643 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.695, G.1117 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: A.692, E.1058, N.1060 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.150, N.151 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herrera, N.G. et al., Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis. Biorxiv (2020)

Release Date

2020-06-10

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein