SMTL ID : 6tcm.1

Crystal structure of the omalizumab Fab - crystal form I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: S.14, K.111, R.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.14, A:K.111 GOL.5: 2 residues within 4Å: Chain B: Y.102 Ligands: PO4.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.53, A:Y.53 Water bridges: A:E.59, B:Y.102 GOL.6: 5 residues within 4Å: Chain B: N.207, K.209, N.212, T.213, K.214 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.207, B:T.213 GOL.7: 3 residues within 4Å: Chain B: S.164, N.205, D.216 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.216 Water bridges: B:S.161, B:S.161 GOL.8: 7 residues within 4Å: Chain B: E.156, P.157, V.158, F.174, P.175, A.176, L.186 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.156, B:V.158, B:V.158, B:A.176 GOL.9: 3 residues within 4Å: Chain B: Y.33, H.101, H.105 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.33, B:Y.33 GOL.10: 4 residues within 4Å: Chain B: V.2, Y.27, R.98 Ligands: PO4.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.98, B:R.98 Water bridges: B:R.98 GOL.11: 12 residues within 4Å: Chain A: Q.164, S.166, S.180, S.181, T.182 Chain B: F.174, P.175, A.176, V.177, S.185, L.186, S.187 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:F.174, B:S.187, A:Q.164, A:S.166, A:S.180, A:T.182

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 3 residues within 4Å: Chain A: K.43, K.46, K.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.43

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

PO4.3: 5 residues within 4Å: Chain A: D.171, K.173 Chain B: S.169, G.170, H.172 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:G.170 Water bridges: B:V.171, B:V.171, A:D.171, A:D.171, A:K.173, A:K.173, A:K.173, A:K.173 Salt bridges: B:H.172, A:K.173 PO4.4: 6 residues within 4Å: Chain B: R.98, S.100, H.101, Y.102 Ligands: GOL.5, GOL.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.100, B:S.100, B:H.101 Water bridges: B:R.98, B:R.98, B:S.100 Salt bridges: B:R.98, B:H.101

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

Related Entries With Identical Sequence