SMTL ID : 5w5n.1

Crystal structure of human IgG4-Sigma2 Fc fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- NAG: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-GAL-MAN-NAG.1: 14 residues within 4Å: Chain A: F.16, F.18, P.19, K.21, E.33, T.35, V.39, D.40, Q.70, N.72, T.74, R.76 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.2, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.18, A:E.33, A:E.33, A:T.35 Water bridges: A:E.33

1 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- NAG- FUC: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-GAL-MAN-NAG-FUC.2: 16 residues within 4Å: Chain B: F.16, F.18, P.19, P.20, K.21, E.33, T.35, V.37, V.39, D.40, Q.70, F.71, N.72, T.74, R.76 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.18, B:K.21, B:K.21, B:E.33, B:E.33 Water bridges: B:D.24, B:E.33, B:F.71 Hydrophobic interactions: B:F.71, B:N.72

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Y.53, K.95, K.97, E.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.95, A:K.97, A:E.108 GOL.5: 5 residues within 4Å: Chain B: Y.53, G.56, K.95, K.97, E.108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.95, B:K.97, B:K.97, B:E.108

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 4 residues within 4Å: Chain B: E.47, V.48, R.67, V.77 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.47, B:V.77 Hydrogen bonds: B:V.48, B:R.67 Salt bridges: B:R.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tam, S.H. et al., Functional, Biophysical, and Structural Characterization of Human IgG1 and IgG4 Fc Variants with Ablated Immune Functionality. Antibodies (2017)

Release Date

2017-09-13

Peptides

Immunoglobulin heavy constant gamma 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Immunoglobulin heavy constant gamma 4