SMTL ID : 5xje.1

Crystal structure of fucosylated IgG1 Fc complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-1-mer

Ligands

2 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: 19 residues within 4Å: Chain A: F.17, F.19, P.20, P.21, K.22, D.25, E.34, T.36, V.38, V.40, D.41, Q.71, N.73, T.75, R.77, K.110 Chain C: T.120, Y.130 Ligands: NAG-FUC.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.19, A:D.25, A:E.34, A:E.34, A:E.34, A:T.36 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.2: 14 residues within 4Å: Chain B: F.17, F.19, P.20, P.21, K.22, D.25, E.34, T.36, V.40, D.41, Q.71, N.73, T.75, R.77 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.19, B:K.22, B:D.25, B:E.34, B:E.34, B:T.36

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.3: 5 residues within 4Å: Chain C: K.118, R.153, L.155, N.160 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.1 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:R.153 Hydrogen bonds: C:R.153

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 5 residues within 4Å: Chain C: H.42, N.43, D.62, S.64, G.65 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.62, C:S.64

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

CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakae, Y. et al., Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fc gamma receptor IIIa. Sci Rep (2017)

Release Date

2017-11-01

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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