SMTL ID : 5d4q.1

Crystal structure of GASDALIE IgG1 Fc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

2 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: 18 residues within 4Å: Chain A: F.16, F.18, P.19, P.20, K.21, D.24, E.33, T.35, V.37, V.39, D.40, Q.70, N.72, T.74, R.76, K.109 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.18, A:K.21, A:K.21, A:D.24, A:E.33, A:E.33 Hydrophobic interactions: A:F.16 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2: 18 residues within 4Å: Chain B: D.14, F.16, F.18, P.19, P.20, K.21, E.33, T.35, V.37, V.39, D.40, N.72, T.74, R.76, K.109 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, FUC.3 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:P.19, B:K.21, B:K.21, B:E.33, B:E.33, B:E.33, B:T.35, B:T.35 Water bridges: B:D.24

1 x FUC: alpha-L-fucopyranose(Non-functional Binders)

FUC.3: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmed, A.A. et al., Structural characterization of GASDALIE Fc bound to the activating Fc receptor Fc gamma RIIIa. J.Struct.Biol. (2016)

Release Date

2016-02-10

Peptides

Ig gamma-1 chain C region: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ig gamma-1 chain C region