SMTL ID : 3v7m.1

Crystal structure of monoclonal human anti-Rhesus D Fc IgG1 T125(YB2/0) in the presence of Zn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- MAN- 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)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN-NAG-GAL-MAN-NAG.1: 13 residues within 4Å: Chain A: F.6, F.8, P.9, P.10, K.11, E.23, T.25, V.29, D.30, Q.60, N.62, T.64, R.66 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.8, A:K.11, A:E.23 Water bridges: A:E.23, A:E.23 NAG-NAG-MAN-MAN-NAG-GAL-MAN-NAG.9: 13 residues within 4Å: Chain B: F.6, F.8, P.9, P.10, K.11, E.23, T.25, V.29, D.30, Q.60, N.62, T.64, R.66 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.8, B:K.11, B:E.23, B:T.25 Water bridges: B:E.23, B:E.23

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.75, L.79, H.200 Ligands: IMD.6, IMD.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.75, A:H.200 ZN.3: 3 residues within 4Å: Chain A: E.48, H.50 Ligands: IMD.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.50 ZN.4: 1 residues within 4Å: Chain A: H.198 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.198, H2O.5, H2O.6 ZN.10: 5 residues within 4Å: Chain B: H.75, L.79, H.200 Ligands: IMD.14, IMD.15 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.75, B:H.200 ZN.11: 3 residues within 4Å: Chain B: E.48, H.50 Ligands: IMD.13 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.50 ZN.12: 1 residues within 4Å: Chain B: H.198 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.198, H2O.11, H2O.11

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 2 residues within 4Å: Chain A: H.50 Ligands: ZN.3 No protein-ligand interaction detected (PLIP) IMD.6: 7 residues within 4Å: Chain A: H.75, Q.76, L.79, N.80, H.200 Ligands: ZN.2, IMD.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.76 IMD.7: 6 residues within 4Å: Chain A: I.18, H.75, N.199, H.200 Ligands: ZN.2, IMD.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.199 IMD.13: 2 residues within 4Å: Chain B: H.50 Ligands: ZN.11 No protein-ligand interaction detected (PLIP) IMD.14: 7 residues within 4Å: Chain B: H.75, Q.76, L.79, N.80, H.200 Ligands: ZN.10, IMD.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.76 IMD.15: 6 residues within 4Å: Chain B: I.18, H.75, N.199, H.200 Ligands: ZN.10, IMD.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.199

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 1 residues within 4Å: Chain A: N.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 GOL.16: 1 residues within 4Å: Chain B: N.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Siberil, S. et al., Effect of zinc on human IgG1 and its Fc gamma R interactions. Immunol.Lett. (2012)

Release Date

2012-02-22

Peptides

Ig gamma-1 chain C region: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ig gamma-1 chain C region