SMTL ID : 7r14.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

7 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.737, G.1159 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.745, L.950 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.950 NAG-NAG.4: 4 residues within 4Å: Chain A: N.1126, T.1128, H.1129, F.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.745, L.950, Q.954 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1126, T.1128, H.1129, F.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.745, L.950, Q.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.829, S.831, Q.832 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: 3 residues within 4Å: Chain A: A.734, N.1102, T.1104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.1102, A:N.1102

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

NAG.9: 1 residues within 4Å: Chain A: N.92 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.308, E.309, N.310 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.359, Q.608 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: G.367, N.371, A.400 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.631 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.644, T.646 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.685 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.829, S.831 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1162 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.61, N.92 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.192, N.193 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: T.137, N.262, T.264 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: E.309, N.310 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.359, Q.608 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.631 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.644, T.646, R.674 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.685 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.737 Chain C: D.824 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.829, S.831 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: E.1100, N.1102 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1162 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: F.370, N.371, A.400, F.402 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.1162 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.1126, H.1129, F.1131 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: A.734, N.1102 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.262 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: E.309, N.310 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.631 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.644 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: H.683, N.685 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: D.824 Chain C: N.737, G.1159 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.359, Q.608 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: F.370, N.371, V.395 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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