SMTL ID : 6tcr.1

Crystal structure of the omalizumab Fab Ser81Arg, Gln83Arg and Leu158Pro light chain mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 9 residues within 4Å: Chain A: Y.102, H.105, W.106, H.107 Chain B: Y.36, M.37, N.38, A.54, S.95 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.38, B:A.54, A:Y.102, A:H.105 EDO.2: 2 residues within 4Å: Chain A: Q.179, S.180 No protein-ligand interaction detected (PLIP) EDO.3: 6 residues within 4Å: Chain A: S.31, G.32, T.53, Y.54, H.101, W.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.31 Water bridges: A:Y.54 EDO.4: 4 residues within 4Å: Chain B: K.43, K.46, K.49 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.46, B:K.46, B:K.49 EDO.5: 7 residues within 4Å: Chain B: Q.41, K.43, K.49, P.63, R.65, F.66 Ligands: EDO.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.41, B:Q.41, B:K.43, B:K.49, B:R.65 Water bridges: B:R.65 EDO.7: 6 residues within 4Å: Chain A: Y.95 Chain B: Q.42, K.43, P.44, G.45, K.46 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.95, B:G.45, B:K.46 EDO.8: 4 residues within 4Å: Chain B: Q.159, N.162, L.185, H.193 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.159, B:Q.159, B:N.162 EDO.9: 3 residues within 4Å: Chain B: S.163, Q.164, E.165 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.165, B:E.165 Water bridges: B:G.161, B:S.163

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

PEG.6: 9 residues within 4Å: Chain B: S.14, V.15, P.84, I.110, K.111, R.112, K.173, D.174, S.175 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.14, B:V.15, B:K.173

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 Ser81Arg, Gln83Arg and Leu158Pro light chain mutant: A
Omalizumab Fab Ser81Arg, Gln83Arg and Leu158Pro light chain mutant: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Omalizumab Fab Ser81Arg, Gln83Arg and Leu158Pro light chain mutant

Omalizumab Fab Ser81Arg, Gln83Arg and Leu158Pro light chain mutant

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