SMTL ID : 3c2s.1

Structural Characterization of a Human Fc Fragment Engineered for Lack of Effector Functions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

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: 14 residues within 4Å: Chain A: F.19, F.21, P.22, P.23, K.24, E.36, T.38, V.42, D.43, Q.73, N.75, T.77, R.79, K.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.21, A:K.24, A:E.36, A:T.38, A:T.38 Water bridges: A:D.27 Hydrophobic interactions: A:K.112 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.6: 14 residues within 4Å: Chain B: F.19, F.21, P.22, P.23, K.24, E.36, T.38, V.42, D.43, Q.73, N.75, T.77, R.79, K.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.21, B:K.24, B:E.36, B:T.38 Water bridges: B:D.27, B:D.27 Hydrophobic interactions: B:K.112

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: H.88, L.92, H.213 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.88, A:H.213, H2O.1, H2O.2 ZN.3: 1 residues within 4Å: Chain A: H.63 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.63, H2O.1, H2O.2 ZN.4: 1 residues within 4Å: Chain A: E.96 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.96, A:E.96 ZN.5: 1 residues within 4Å: Chain A: E.123 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.123, A:E.123, H2O.2, H2O.3 ZN.7: 3 residues within 4Å: Chain B: H.88, L.92, H.213 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.88, B:H.213, H2O.4, H2O.5 ZN.8: 1 residues within 4Å: Chain B: H.63 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.63, H2O.4, H2O.5 ZN.9: 1 residues within 4Å: Chain B: E.96 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.96, B:E.96 ZN.10: 1 residues within 4Å: Chain B: E.123 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.123, B:E.123, H2O.5, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oganesyan, V. et al., Structural characterization of a human Fc fragment engineered for lack of effector functions. Acta Crystallogr.,Sect.D (2008)

Release Date

2008-08-19

Peptides

IGHM protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

IGHM protein