SMTL ID : 7r16.1

Beta Variant SARS-CoV-2 Spike with 1 Erect RBD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

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: 3 residues within 4Å: Chain A: N.745, L.950, Q.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.829, S.831 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.1126, T.1128, H.1129 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.745, L.950, Q.954, Q.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.1126, T.1128, H.1129, F.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.829, S.831, Q.832 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: Y.59, N.92 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.265, I.266, T.267 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.359 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.631 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.644, T.646 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: H.683, V.684, N.685 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.737 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.1102 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.1162 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: E.309, N.310 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: Y.59, F.90, N.92 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: T.139, N.265, T.267 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.359, Q.608 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.644, T.646 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: H.683, N.685 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.829, S.831, Q.832 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.1102 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.1162 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: E.309, N.310 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.1162 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.1126, T.1128 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: A.734, E.1100, N.1102 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.310 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: E.337, N.631 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.644, T.646 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.737 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.745, L.950, Q.954 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.685 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wrobel, A.G. et al., Evolution of the SARS-CoV-2 spike protein in the human host. Nat Commun (2022)

Release Date

2022-03-09

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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