SMTL ID : 5mol.1

Human IgE-Fc crystal structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-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: 14 residues within 4Å: Chain A: Y.119, S.121, R.122, S.124, T.135, T.137, L.139, V.141, D.142, Q.172, N.174, T.176, T.178 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.121, A:T.135, A:T.137, A:Y.119, A:Y.119 Water bridges: A:S.124

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN-MAN.2: 13 residues within 4Å: Chain B: R.114, Y.119, S.121, R.122, P.123, S.124, L.139, V.141, D.142, Q.172, N.174, T.176, T.178 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.141, B:T.178 Hydrogen bonds: B:R.114, B:Y.119

2 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.3: 2 residues within 4Å: Chain A: D.51, T.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.89, A:T.89 PG0.8: 4 residues within 4Å: Chain B: K.132, N.163, V.185, G.186 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.163 Water bridges: B:V.185, B:T.187, B:T.187

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

EDO.4: 5 residues within 4Å: Chain A: R.122, P.123, D.253 Ligands: NAG-NAG-BMA-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.253 Water bridges: A:R.122 EDO.5: 2 residues within 4Å: Chain A: Q.45, T.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.45 EDO.6: 2 residues within 4Å: Chain A: E.50, Q.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.50, A:E.50 Water bridges: A:R.88 EDO.10: 4 residues within 4Å: Chain A: Q.74 Chain B: L.33, L.35, Q.74 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.74 EDO.11: 2 residues within 4Å: Chain B: A.221, A.222 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.222

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

PEG.7: 4 residues within 4Å: Chain A: H.25 Chain B: Q.172, R.173, G.175 No protein-ligand interaction detected (PLIP) PEG.12: 4 residues within 4Å: Chain B: R.269, E.290, T.292, E.295 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.290, B:E.290, B:E.295

1 x AE3: 2-(2-ETHOXYETHOXY)ETHANOL(Non-covalent)

AE3.9: 9 residues within 4Å: Chain B: I.254, S.255, V.256, D.267, T.272, T.273, Q.274, P.275, V.285 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.256, B:T.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dore, K.A. et al., Thermal sensitivity and flexibility of the C epsilon 3 domains in immunoglobulin E. Biochim. Biophys. Acta (2017)

Release Date

2018-01-10

Peptides

Ig epsilon chain C region: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ig epsilon chain C region

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