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

IgE-Fc in complex with omalizumab variant C02

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-1-1-2-mer

Ligands

1 x NAG- NAG- BMA- MAN: 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.1: 6 residues within 4Å: Chain C: Y.14, L.34, Q.67, R.68, N.69, T.71 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: N.29, T.31, G.75, N.78 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.78 Hydrogen bonds: A:N.29, A:T.31, A:S.76

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

EDO.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 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.100, A:S.35, A:S.35, A:S.52, A:N.60

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 6 residues within 4Å: Chain A: N.101, H.108 Chain B: Y.55, E.61 Chain C: T.90, Q.92 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:N.101, C:T.90, C:Q.92 Salt bridges: A:H.108 Water bridges: C:T.90

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 variant C02 VH: A
omalizumab variant C02 VL: B
Immunoglobulin heavy constant epsilon: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
B

D
B

omalizumab variant C02 VH

omalizumab variant C02 VL

Immunoglobulin heavy constant epsilon

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