SMTL ID : 7r15.1

Alpha Variant SARS-CoV-2 Spike with 2 Erect RBDs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 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.308, E.309, N.310 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.745 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: N.359, I.360, Q.608 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: Y.59, N.92 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.262 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.359, Q.608, L.610 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.631 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.644 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.737 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.829, S.831 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: A.734, N.1102 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1162 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: G.367, N.371 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.151, T.153, V.156 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.92 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: E.161, N.192, N.193 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.308, E.309, N.310 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.631 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.644 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.737, N.738 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.745 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.829, S.831 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: E.1100, N.1102 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.1162 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: F.366, G.367, F.370, N.371 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: N.151, T.153, N.154, E.182, F.185 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: N.1126, T.1128, H.1129, F.1131 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.92 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: E.161, N.192, N.193 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: E.309, N.310 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.631 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.644 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.737 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.745 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.829, S.831 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.1162 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.151, T.153, N.154, F.185 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: P.358, N.359, Q.608 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: F.366, G.367, N.371, V.395 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.1126, T.1128, F.1131, Y.1138 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

2022-03-02

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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