SMTL ID : 7shy.2 (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- MAN- FUC: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(2-3)-[alpha-L-fucopyranose-(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-MAN-FUC.1: 13 residues within 4Å: Chain C: Y.41, S.43, R.44, S.46, L.61, V.63, D.64, Q.94, N.96, T.98, T.100, I.176, Q.196 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.196, C:S.43, C:I.176, C:Y.41, C:Y.41, C:T.100, C:T.100

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.2: 15 residues within 4Å: Chain C: R.198 Chain F: Y.41, S.43, R.44, S.46, L.61, D.64, Q.94, R.95, N.96, T.98, T.100, I.176, T.194, Q.196 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.41, F:T.100

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: S.35, N.37, W.49, S.52, N.60, W.107 Chain B: D.100, Y.102 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.35, A:S.35 Water bridges: B:D.100

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

NAG.4: 1 residues within 4Å: Chain C: N.73 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.73 NAG.5: 2 residues within 4Å: Chain E: D.34 Chain F: N.73 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:D.34, F:N.73

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: AD
Omalizumab VL: BE
IgE Fc: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

D
E

B
D

E
F

C
A

F
B

Omalizumab VH

Omalizumab VL

IgE Fc

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