SMTL ID : 6tcn.1 (1 other biounit)

Crystal structure of the omalizumab Fab - crystal form II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.43, A:K.46, 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:H.101 Salt bridges: B:R.98, B:H.101

7 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.41, A:K.43, A:K.49, A:R.65, A:E.85 EDO.3: 3 residues within 4Å: Chain A: P.8, S.9, S.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.9, A:S.10 EDO.4: 3 residues within 4Å: Chain A: P.63, R.65, E.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.65, A:R.65, A:E.85 EDO.5: 2 residues within 4Å: Chain A: P.63, S.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.64 EDO.7: 6 residues within 4Å: Chain A: T.182 Chain B: L.149, V.177, S.185, L.186, S.187 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.182 Water bridges: A:T.182, B:S.187, B:S.187, B:S.187 EDO.8: 5 residues within 4Å: Chain B: S.7, G.8, G.9, T.115 Ligands: PEG.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.8, B:G.9, B:T.115, B:T.115 EDO.9: 2 residues within 4Å: Chain B: R.87, A.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.88 Water bridges: B:E.89

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 6 residues within 4Å: Chain B: Q.113, G.114, T.115, L.116, P.157 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.113, B:L.116

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: A
Omalizumab Fab: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Omalizumab Fab

Omalizumab Fab

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