SMTL ID : 6tco.2 (1 other biounit)

Crystal structure of the omalizumab Fab Leu158Pro light chain mutant - crystal form I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: Q.41, K.43, K.46, K.49 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.43, A:K.49 SO4.6: 4 residues within 4Å: Chain B: R.98, S.100, H.101, Y.102 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.101 Water bridges: B:R.98, B:S.100 Salt bridges: B:R.98, B:H.101

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

EDO.2: 9 residues within 4Å: Chain A: Q.41, K.43, K.49, P.63, R.65, F.66, E.85, D.86 Ligands: SO4.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.41, A:K.43, A:K.49, A:K.49, A:R.65, A:D.86 EDO.3: 6 residues within 4Å: Chain A: L.50, Y.53, E.59 Chain B: S.100, Y.102, H.107 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.59, B:S.100 EDO.4: 3 residues within 4Å: Chain A: S.125, D.126, E.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.126, A:E.127 EDO.5: 2 residues within 4Å: Chain A: S.69, G.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.70 Water bridges: A:G.68, A:S.71 EDO.7: 5 residues within 4Å: Chain B: V.24, S.25, G.26, Y.27, N.77 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.25, B:G.26, B:Y.27, B:Y.27 EDO.8: 2 residues within 4Å: Chain B: P.62, K.65 No protein-ligand interaction detected (PLIP) EDO.9: 6 residues within 4Å: Chain A: T.182 Chain B: L.149, V.177, S.185, L.186, S.187 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.187, A:T.182 Water bridges: B:S.187, B:S.187, B:S.187 EDO.10: 4 residues within 4Å: Chain B: G.8, V.12, L.18, R.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.19 EDO.11: 4 residues within 4Å: Chain B: S.7, G.8, G.9, T.115 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.8, B:G.9, B:T.115, B:T.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mitropoulou, A.N. et al., Engineering the Fab fragment of the anti-IgE omalizumab to prevent Fab crystallization and permit IgE-Fc complex crystallization. Acta Crystallogr.,Sect.F (2020)

Release Date

2020-03-18

Peptides

Omalizumab Fab Leu158Pro light chain mutant: A
Omalizumab Fab Leu158Pro light chain mutant: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Omalizumab Fab Leu158Pro light chain mutant

Omalizumab Fab Leu158Pro light chain mutant

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