SMTL ID : 5mok.1

Crystal structure of human IgE-Fc epsilon 3-4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

1 x NAG- NAG- BMA- MAN: 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.1: 7 residues within 4Å: Chain A: Y.15, S.17, L.35, Q.68, N.70, T.72, T.74 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.17, A:S.17, A:Y.15, A:Y.15, A:T.74

2 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: 9 residues within 4Å: Chain B: Y.15, L.35, V.37, D.38, Q.68, N.70, T.72, T.74, Q.170 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.15, B:Y.15 NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 17 residues within 4Å: Chain D: Y.15, S.17, R.18, P.19, S.20, L.35, V.37, Q.68, N.70, T.72, T.74, E.148, D.149, I.150, T.168, Q.170, P.171 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.170, D:Q.170, D:R.172, D:Y.15, D:T.74

1 x 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

NAG-BMA-MAN-MAN.3: 5 residues within 4Å: Chain C: Y.15, L.35, V.37, T.74, Q.170 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.170, C:S.13, C:S.13, C:Y.15

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

PEG.5: 4 residues within 4Å: Chain A: R.165, T.188, A.190, E.191 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.188 Hydrogen bonds: A:T.188 PEG.10: 5 residues within 4Å: Chain D: L.161, P.162, A.164, R.165, E.191 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.165, D:E.191

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

EDO.6: 4 residues within 4Å: Chain A: D.23, R.27, T.31, T.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.23, A:R.27, A:T.31 EDO.7: 2 residues within 4Å: Chain A: R.133, D.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.133, A:D.134 EDO.8: 4 residues within 4Å: Chain C: H.156, N.157, V.159, L.161 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.156, C:V.159 Water bridges: C:H.156, C:N.157, C:E.191 EDO.9: 5 residues within 4Å: Chain C: Y.122, A.123, F.124, R.215 Chain D: P.127 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.123 Water bridges: C:A.123 EDO.11: 3 residues within 4Å: Chain D: R.201, S.210, T.212 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.201, D:S.210, D:S.210 Water bridges: D:R.201

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ig epsilon chain C region

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