SMTL ID : 8gdr.1

SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21B10

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

4 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 D: N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain D: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain D: N.736, L.941, Q.945, Q.1090 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.941 NAG-NAG.4: 3 residues within 4Å: Chain D: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.301 Chain E: K.577 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.350, Q.599 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.635, C.636 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.728, G.1150 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.736, Q.945 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.1117, G.1118, H.1120, F.1122 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.1153 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.676 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.820, S.822, Q.823 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.1093 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: K.576 Chain D: N.301 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain D: N.676 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain D: N.635, T.637 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain D: N.728, G.1150 Chain E: D.815 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain D: A.725, N.1093 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain D: N.622 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain D: N.362 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain E: N.350, I.351, Q.599 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain E: N.622 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain E: N.635 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain E: N.676 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain E: N.728, G.1150 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain E: N.736, Q.1090 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain E: N.1153 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain E: G.358, F.361, N.362, V.386 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain E: N.1117, G.1118 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain A: Q.914 Chain E: A.732, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: N.820, S.822, Q.823 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patel, A. et al., Elucidating the mechanism of SARS-CoV-2 Omicron variant escape from a RBD class-3 human antibody. To Be Published

Release Date

2024-03-13

Peptides

Spike glycoprotein: ADE
Monoclonal antibody 002-S21B10 heavy chain variable domain: BF
Monoclonal antibody 002-S21B10 light chain variable domain: CG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

E
F

B
C

F
H

C
D

G
J

Spike glycoprotein

Monoclonal antibody 002-S21B10 heavy chain variable domain

Monoclonal antibody 002-S21B10 light chain variable domain