SMTL ID : 5moj.1

Crystal structure of IgE-Fc epsilon 3-4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

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: 7 residues within 4Å: Chain A: Y.15, S.17, L.35, V.37, N.70, T.72 Ligands: NAG-NAG-BMA-MAN-MAN.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.35 Hydrogen bonds: A:Y.15, A:Y.15 NAG-NAG-BMA-MAN-MAN.2: 10 residues within 4Å: Chain B: Y.15, L.35, V.37, D.38, Q.68, N.70, T.72, T.74, Q.170 Ligands: NAG-NAG-BMA-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.170, B:Y.15

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

SO4.3: 2 residues within 4Å: Chain A: H.60, S.61 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.61, A:S.61 Salt bridges: A:H.60 SO4.4: 5 residues within 4Å: Chain A: T.174, K.175, G.176 Chain B: R.184, E.186 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.144, A:T.174, A:K.175, A:G.176 Salt bridges: B:R.184 SO4.5: 5 residues within 4Å: Chain A: I.150, S.151, V.152, H.166, T.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.152 Salt bridges: A:H.166 SO4.8: 3 residues within 4Å: Chain B: Q.59, H.60, S.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.61 Salt bridges: B:H.60 SO4.9: 3 residues within 4Å: Chain B: G.82, T.83, R.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.83, B:T.83, B:R.84 SO4.10: 3 residues within 4Å: Chain B: E.158, V.159, Q.160 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.160 SO4.11: 5 residues within 4Å: Chain A: R.184, E.186 Chain B: T.174, K.175, G.176 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.174, B:K.175, B:G.176 Salt bridges: A:R.184

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

EDO.6: 6 residues within 4Å: Chain A: T.169, Q.170, R.172 Chain B: T.169, Q.170, R.172 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.170, A:R.172, A:R.172, B:Q.170, B:R.172 Water bridges: A:T.169 EDO.7: 4 residues within 4Å: Chain A: G.82, T.83, R.84, D.85 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.83, A:T.83, A:R.84, A:D.85, A:D.85

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

PEG.12: 6 residues within 4Å: Chain B: S.20, F.22, S.151, V.152, H.166, T.168 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.20, B:S.20, B:V.152, B:T.168

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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