SMTL ID : 7ydy.1

SARS-CoV-2 Spike (6P) in complex with 1 R1-32 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

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: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: F.43, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain A: N.331, I.332, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.709, N.710 Chain B: D.796 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.1098, T.1100, F.1103, Y.1110 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: K.558 Chain B: F.43, N.282 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: P.330, N.331, Q.580 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.709, N.710 Chain C: D.796 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.1098, T.1100, F.1103, Y.1110 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: I.1132, N.1134 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain C: N.282 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: P.330, N.331 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: T.602, N.603 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: D.796 Chain C: N.709 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: N.1098, T.1100, F.1103, Y.1110 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: I.1132, N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, P. et al., SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope. Nat Microbiol (2022)

Release Date

2022-08-24

Peptides

Spike glycoprotein: ABC
Heavy chain of R1-32 Fab: D
Light chain of R1-32 Fab: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

Heavy chain of R1-32 Fab

Light chain of R1-32 Fab

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