SMTL ID : 4l4j.1

Crystal structure of fc-fragment of human IgG2-Sigma antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- MAN- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-MAN-FUC.1: 12 residues within 4Å: Chain A: F.15, F.17, K.20, T.34, V.36, V.38, D.39, Q.69, F.70, N.71, T.73, R.75 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.71 Water bridges: A:F.70, A:R.75 Hydrogen bonds: A:K.20, A:K.20

1 x NAG- NAG- BMA- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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(Non-functional Binders)

NAG-NAG-BMA-MAN-NAG.2: 5 residues within 4Å: Chain B: F.15, F.17, K.20, V.38, R.75 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.20 Water bridges: B:K.20, B:K.20, B:K.20, B:K.20, B:T.34

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: K.144, D.173, S.174, D.175 Chain B: Q.136, N.164, T.185 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.144, A:K.144, A:S.174, B:N.164, B:K.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vafa, O. et al., An engineered Fc variant of an IgG eliminates all immune effector functions via structural perturbations. Methods (2014)

Release Date

2013-08-28

Peptides

Ig gamma-2 chain C region: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ig gamma-2 chain C region