SMTL ID : 5yc5.1

Crystal structure of human IgG-Fc in complex with aglycan and optimized Fc gamma receptor IIIa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

hetero-2-1-mer

Ligands

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.1: 15 residues within 4Å: Chain A: F.18, F.20, P.21, P.22, K.23, E.35, T.37, V.39, V.41, D.42, Q.72, N.74, T.76, R.78, K.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.20, A:K.23, A:K.23, A:E.35, A:E.35, A:E.35, A:T.37 Water bridges: A:K.23, A:D.26 Hydrophobic interactions: A:F.18

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

NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2: 12 residues within 4Å: Chain B: F.18, F.20, K.23, T.37, V.39, V.41, D.42, Q.72, Y.73, N.74, R.78, K.111 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.73 Hydrogen bonds: B:R.78, B:K.23, B:K.23

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: K.97, K.99, E.110 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kiyoshi, M. et al., Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered Fc gamma Receptor IIIa-Immobilized Column. Sci Rep (2018)

Release Date

2018-03-21

Peptides

Immunoglobulin gamma-1 heavy chain: AB
Low affinity immunoglobulin gamma Fc region receptor III-A: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Immunoglobulin gamma-1 heavy chain

Low affinity immunoglobulin gamma Fc region receptor III-A

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