SMTL ID : 7lyk.1

South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 2-RBD-up conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: V.656, N.657, N.658 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: N.717, F.718, Q.926, Q.1071 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: N.717, Q.1071 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: A.706, N.1074 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: I.1132, N.1134 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: N.801, S.803 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gobeil, S.M. et al., Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity. Science (2021)

Release Date

2021-03-31

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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