SMTL ID : 7shy.1 (1 other biounit)

IgE-Fc in complex with omalizumab scFv

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-2-2-2-mer

Ligands

1 x NAG- NAG- BMA- MAN- BMA- MAN: beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-BMA-MAN.1: 12 residues within 4Å: Chain E: Y.41, S.43, R.44, S.46, D.49, L.61, V.63, D.64, Q.94, N.96, T.98, T.100 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.43, E:S.43, E:D.49, E:Y.41, E:Y.41

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 7 residues within 4Å: Chain F: Y.41, V.63, D.64, Q.94, N.96, T.98 Ligands: MAN.3 No protein-ligand interaction detected (PLIP)

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.3: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.2, NAG-NAG-BMA-MAN.2 No protein-ligand interaction detected (PLIP)

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

NAG.4: 1 residues within 4Å: Chain F: N.73 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pennington, L.F. et al., Directed evolution of and structural insights into antibody-mediated disruption of a stable receptor-ligand complex. Nat Commun (2021)

Release Date

2021-12-15

Peptides

Omalizumab VH: AB
Omalizumab VL: CD
IgE Fc: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
K

C
J

D
L

E
G

F
H

Omalizumab VH

Omalizumab VL

IgE Fc

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