SMTL ID : 7upl.1

SARS-Cov2 Omicron varient 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

13 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: 5 residues within 4Å: Chain A: N.1095, G.1096, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain C: N.798, Q.801 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.801 NAG-NAG.3: 9 residues within 4Å: Chain A: N.231, T.233 Chain C: R.454, S.456, N.457, L.458, K.459, E.462, D.464 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.456, C:S.456 NAG-NAG.4: 1 residues within 4Å: Chain A: N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.714, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.798 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: K.459 Chain B: N.231, T.233 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.714, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.231, T.233 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.714, F.715, N.916, L.919, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain A: Q.892 Chain C: A.703, N.1071 No protein-ligand interaction detected (PLIP)

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

NAG.14: 4 residues within 4Å: Chain A: F.335, D.336, N.340 Chain F: R.59 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.120 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.328 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.613 Chain B: K.832 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.706 Chain B: Y.793 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: S.110, E.130, F.131, Q.132, N.160 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.613, Q.641 Chain C: I.831 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.1095, T.1097, H.1098 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: A.703, N.1071 Chain C: Q.892 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: E.278, N.279 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: Q.833 Chain C: N.613, T.615 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.1095, T.1097 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: F.131, N.160, T.162 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.654 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 light chain: DG
mAb 002-S21F2 heavy chain: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

G
I

E
E

F
F

Spike glycoprotein

mAB 002-S21F2 light chain

mAb 002-S21F2 heavy chain

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