SMTL ID : 7u0p.1

SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21F2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

5 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: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: N.717, L.922 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 B: F.342, N.343 Chain E: R.59 No protein-ligand interaction detected (PLIP)

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

NAG.6: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.717 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1098 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.282, T.284 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.709 Chain C: D.796 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.1074 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 C: N.331, Q.580 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.709, I.1130 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.717 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: F.342, N.343 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, S. et al., Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody. Sci Adv (2022)

Release Date

2022-08-10

Peptides

Spike glycoprotein: ABC
mAb 002-S21F2 Heavy chain: DE
mAb 002_S21F2 light chain: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
D

F
I

G
F

Spike glycoprotein

mAb 002-S21F2 Heavy chain

mAb 002_S21F2 light chain

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