SMTL ID : 7lyo.1

South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 1-RBD-up conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: N.165 Chain C: Y.351, I.468, T.470 Ligand excluded by PLIP NAG.3: 8 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, S.459, N.460, K.462, E.465 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.280, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: F.338, F.342, N.343, L.368 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain B: S.112, K.113, E.132, N.164, N.165 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.280, N.282 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.709, I.1130 Chain C: D.796 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: F.338, G.339, N.343 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.40: 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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