SMTL ID : 5hys.2 (1 other biounit)

Structure of IgE complexed with omalizumab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.1: 9 residues within 4Å: Chain E: R.10, Y.15, L.35, V.37, D.38, Q.68, R.69, N.70, T.72 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.15, E:Y.15 NAG-NAG-BMA-MAN-MAN.2: 10 residues within 4Å: Chain F: P.9, Y.15, L.35, V.37, D.38, Q.68, N.70, T.72, T.74, Q.170 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.170, F:Q.170, F:Y.15, F:T.74

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

SO4.3: 3 residues within 4Å: Chain A: P.14, S.120, S.121 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: N.59, Y.60, K.65 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: D.216, K.217, K.218 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: S.7, G.8, G.9, T.115, K.209 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain B: K.43, K.46, K.49 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain B: S.12, K.111 Chain D: S.9, S.10, K.107 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: P.131 Chain B: S.125, D.126, E.127 Ligand excluded by PLIP SO4.10: 1 residues within 4Å: Chain B: S.64 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: S.140 Chain B: S.118, V.119, K.211 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain B: S.9, S.10, K.107 Chain D: S.12, K.111 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain C: T.115, L.116, P.157, K.209 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain C: D.216, K.217, K.218 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain D: K.43, K.46, K.49 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain B: K.149 Chain D: Q.159, S.160, G.161, N.162, S.163 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain C: P.131 Chain D: S.125, D.126, E.127 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain D: Q.27, S.28 Chain E: G.44, T.45 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain D: S.69, G.70, S.71 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain E: G.82, T.83, R.84 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain E: P.162, D.163 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain E: R.52, K.56, D.85 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain E: S.20, I.150, S.151 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain E: T.169, Q.170, R.172 Chain F: T.169, Q.170, R.172 Ligand excluded by PLIP SO4.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain F: G.82, T.83, R.84 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain E: N.8 Chain F: M.106, R.107, S.108 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain B: S.69, G.70 Chain F: R.103 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pennington, L.F. et al., Structural basis of omalizumab therapy and omalizumab-mediated IgE exchange. Nat Commun (2016)

Release Date

2016-06-01

Peptides

Epididymis luminal protein 214: AC
Uncharacterized protein: BD
Ig epsilon chain C region: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
E

B
D

D
F

E
J

F
K

Epididymis luminal protein 214

Uncharacterized protein

Ig epsilon chain C region

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