SMTL ID : 5vgp.1

Fc fragment of human IgG1 antibody, from NIST mAb

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

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.17, F.19, P.20, K.22, E.34, T.36, V.38, V.40, D.41, Q.71, N.73, T.75, R.77 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2, NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.73 Water bridges: A:Y.72, A:K.22 Hydrogen bonds: A:K.22, A:D.25, A:E.34, A:E.34, A:E.34, A:T.36

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.17, F.19, K.22, T.36, V.40, D.41, Q.71, N.73, T.75, R.77, K.110 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.71, B:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gallagher, D.T. et al., Structure of the Fc fragment of the NIST reference antibody RM8671. Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2018-04-18

Peptides

Human Fc fragment with G1F/G0F glycan: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Human Fc fragment with G1F/G0F glycan