SMTL ID : 7yvp.1

Omicron BA.4/5 SARS-CoV-2 S in complex with TH272/281 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-3-mer

Ligands

37 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 1 residues within 4Å: Chain G: N.234 Ligand excluded by PLIP NAG.2: 5 residues within 4Å: Chain G: S.112, T.114, Q.115, E.132, N.165 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain G: N.280, N.282 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain G: N.709 Chain H: Y.796 Ligands: NAG.11 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain G: N.657 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain G: N.603 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain G: N.1074 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain G: I.1132, N.1134 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain G: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain G: N.616 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain G: N.709 Ligands: NAG.4 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain G: N.801, S.803 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain H: N.657 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain H: R.328, N.331, Q.580, T.581 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain H: N.603 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain H: N.1074 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain H: N.1134 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain H: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain H: N.616 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain H: N.709 Ligands: NAG.25 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain H: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain H: T.108, N.234, T.236 Ligand excluded by PLIP NAG.23: 7 residues within 4Å: Chain H: S.112, K.113, T.114, E.132, A.163, N.164, N.165 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain H: N.282 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain H: N.709 Chain I: Y.796 Ligands: NAG.20 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain G: I.794 Chain I: N.709 Ligands: NAG.33 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain I: N.657 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain I: N.603 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain I: N.1074 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain I: N.1134 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain I: N.1098, H.1101 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain I: N.616 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain I: N.709 Ligands: NAG.26 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain I: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain I: N.234 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain I: S.112, K.113, N.165 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain I: E.281, N.282 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Y. et al., Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun (2023)

Release Date

2023-06-28

Peptides

TH272 Fab heavy chain: AC
TH272 Fab light chain: BD
TH281 Fab light chain: EJ
TH281 Fab heavy chain: FK
Spike glycoprotein: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

C
L

B
J

D
M

E
O

J
H

F
P

K
K

G
A

H
B

I
C

TH272 Fab heavy chain

TH272 Fab light chain

TH281 Fab light chain

TH281 Fab heavy chain

Spike glycoprotein

Related Entries With Identical Sequence