SMTL ID : 8xx0.1

Crystal structure of anti-IgE antibody HMK-12 Fab complexed with IgE F(ab')2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

2 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: 7 residues within 4Å: Chain C: T.237, Q.239, Q.269, K.285, N.287 Chain F: D.56 Ligands: BOG.20 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:D.56 NAG-NAG.12: 7 residues within 4Å: Chain B: D.56 Chain G: T.237, Q.239, Q.269, K.285, N.287 Ligands: BOG.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.56

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: S.116, I.117, F.118, K.207 Chain B: P.134 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: Q.37, K.39, K.45, L.47, F.62, D.82 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: Q.55, G.57 Ligands: EDO.8 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: M.4, F.98, G.99, S.100 Chain B: K.46, L.47 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain B: W.196, E.199, K.217 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain B: N.89, T.92, V.119, L.178 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: Q.55 Chain B: R.99, Y.102, D.109 Ligands: EDO.4 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain C: I.263, D.265, T.266, N.287, Q.292 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain D: S.32, N.33, W.93, Y.94, S.95 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain E: S.116, I.117, F.118, K.207 Chain F: P.134 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain E: Q.37, K.39, K.45, L.47, F.62, D.82 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain E: Q.55, G.57 Ligands: EDO.19 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain E: M.4, F.98, G.99, S.100 Chain F: K.46, L.47 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain F: W.196, E.199, K.217 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain F: N.89, T.92, V.119, L.178 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain E: Q.55 Chain F: R.99, Y.102, D.109 Ligands: EDO.15 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain G: I.263, D.265, T.266, N.287, Q.292 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain H: S.32, N.33, W.93, Y.94, S.95 Ligand excluded by PLIP

2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.9: 5 residues within 4Å: Chain B: D.56, G.57, R.73 Chain C: E.219 Ligands: NAG-NAG.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.56, B:R.73 BOG.20: 5 residues within 4Å: Chain F: D.56, G.57, R.73 Chain G: E.219 Ligands: NAG-NAG.1 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.56, F:R.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirano, T. et al., Allosteric inhibition of IgE-Fc epsilon RI interactions by simultaneous targeting of IgE F(ab')2 epitopes. Commun Biol (2024)

Release Date

2024-07-31

Peptides

anti-IgE antibody HMK-12 Fab light chain: AE
anti-IgE antibody HMK-12 Fab heavy chain: BF
SPE7 immunoglobulin E F(ab')2 heavy chain: CG
SPE7 immunoglobulin E F(ab')2 light chain: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

E
L

B
H

F
H

C
A

G
A

D
B

H
B

anti-IgE antibody HMK-12 Fab light chain

anti-IgE antibody HMK-12 Fab heavy chain

SPE7 immunoglobulin E F(ab')2 heavy chain

SPE7 immunoglobulin E F(ab')2 light chain