SMTL ID : 1o0v.1

The crystal structure of IgE Fc reveals an asymmetrically bent conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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.1: 18 residues within 4Å: Chain A: Y.119, S.121, R.122, T.135, I.136, T.137, L.139, V.141, D.142, Q.172, N.174, T.176, T.178, Q.274 Chain B: S.86, R.88, R.276 Ligands: GOL.7 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.88, B:R.88, A:Q.274, A:Y.119, A:Y.119 Hydrophobic interactions: A:T.178

1 x NAG- NAG- BMA- MAN- MAN- BMA- MAN: alpha-D-mannopyranose-(1-3)-[beta-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-BMA-MAN.2: 15 residues within 4Å: Chain B: R.114, S.117, Y.119, S.121, R.122, P.123, S.124, L.139, V.141, D.142, Q.172, N.174, T.176, T.178, Q.274 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.122, B:S.117, B:S.117 Water bridges: B:S.121, B:S.121, B:I.254 Hydrophobic interactions: B:L.139, B:V.141, B:T.178

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

SO4.3: 4 residues within 4Å: Chain A: D.21, G.22 Chain B: S.104, R.173 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.22, B:S.104, B:R.173 SO4.4: 3 residues within 4Å: Chain A: R.199 Chain B: G.23, H.25 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.199, B:H.25 SO4.5: 4 residues within 4Å: Chain A: G.186, T.187, R.188, D.189 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.187, A:R.188, A:D.189 Salt bridges: A:R.188 SO4.6: 4 residues within 4Å: Chain A: T.273, Q.274, R.276 Chain B: R.276 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.274, A:Q.274, A:Q.274 Water bridges: B:T.273, B:Q.274 Salt bridges: B:R.276, A:R.276

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: S.124, I.254, S.255 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.124 Water bridges: A:D.127, A:D.127 GOL.8: 9 residues within 4Å: Chain A: T.230, P.231, E.232, W.233, S.236, K.239, R.240, T.241 Chain B: Y.226 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.230, A:T.230, A:W.233, A:S.236, A:T.241, A:T.241, B:Y.226, B:Q.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wan, T. et al., The crystal structure of IgE Fc reveals an asymmetrically bent conformation. NAT.IMMUNOL. (2002)

Release Date

2002-09-18

Peptides

Immunoglobulin heavy chain epsilon-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Immunoglobulin heavy chain epsilon-1