SMTL ID : 3v8c.1

Crystal structure of monoclonal human anti-rhesus D Fc IgG1 t125(yb2/0) double mutant (H310 and H435 in K)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

homo-dimer

Ligands

1 x MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-NAG.1: 3 residues within 4Å: Chain B: F.6 Ligands: MAN.10, MAN.15 No protein-ligand interaction detected (PLIP)

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG.2: 6 residues within 4Å: Chain A: V.29, D.30, Q.60, N.62, T.64 Ligands: NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.30, A:N.62, A:N.62 NAG.3: 5 residues within 4Å: Chain A: F.6, V.29 Ligands: NAG.2, MAN.5, MAN.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.66 NAG.8: 5 residues within 4Å: Chain A: F.8, K.11, T.25 Ligands: MAN.7, GAL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.11, A:K.11 NAG.11: 2 residues within 4Å: Ligands: MAN.10, MAN.15 No protein-ligand interaction detected (PLIP) NAG.12: 5 residues within 4Å: Chain B: V.29, D.30, N.62, T.64 Ligands: NAG.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.30, B:N.62, B:T.64 NAG.14: 6 residues within 4Å: Chain B: S.4, F.6, V.29 Ligands: NAG.12, MAN.15, MAN.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.4, B:S.4 NAG.17: 5 residues within 4Å: Chain B: F.8, K.11, T.25 Ligands: MAN.16, GAL.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.11, B:K.11

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Ligands: GOL.6 No protein-ligand interaction detected (PLIP) GOL.6: 1 residues within 4Å: Ligands: GOL.4 No protein-ligand interaction detected (PLIP) GOL.13: 1 residues within 4Å: Chain B: H.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.198

5 x MAN: alpha-D-mannopyranose(Non-covalent)(Non-functional Binders)

MAN.5: 5 residues within 4Å: Chain A: F.6, F.8 Ligands: NAG.3, MAN.7, MAN.10 No protein-ligand interaction detected (PLIP) MAN.7: 3 residues within 4Å: Ligands: NAG.3, MAN.5, NAG.8 No protein-ligand interaction detected (PLIP) MAN.10: 5 residues within 4Å: Chain A: F.6 Ligands: MAN-NAG.1, MAN.5, NAG.11, MAN.15 No protein-ligand interaction detected (PLIP) MAN.15: 7 residues within 4Å: Chain B: F.6, F.8 Ligands: MAN-NAG.1, MAN.10, NAG.11, NAG.14, MAN.16 No protein-ligand interaction detected (PLIP) MAN.16: 4 residues within 4Å: Chain B: F.8 Ligands: NAG.14, MAN.15, NAG.17 No protein-ligand interaction detected (PLIP)

2 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.9: 10 residues within 4Å: Chain A: F.8, P.9, P.10, K.11, D.14, T.21, P.22, E.23, T.25 Ligands: NAG.8 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:P.9, A:K.11, A:K.11, A:T.21, A:E.23, A:T.25, A:T.25, A:T.25 GAL.18: 8 residues within 4Å: Chain B: F.8, P.9, P.10, K.11, E.23, V.24, T.25 Ligands: NAG.17 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.11, B:K.11, B:T.25, B:T.25, B:T.25

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
B

Ig gamma-1 chain C region