SMTL ID : 7q3p.1

Crystal structure of IgG1-Fc-MST-HN (efgartigimod)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

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

NAG-FUC.1: 6 residues within 4Å: Chain A: V.44, D.45, Q.75, N.77, T.79 Ligands: NAG-BMA-MAN-NAG.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.45, A:D.45, A:N.77 Water bridges: A:D.45 NAG-FUC.4: 7 residues within 4Å: Chain C: V.44, D.45, Q.75, Y.76, N.77, T.79 Ligands: NAG-BMA-MAN-MAN.5 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.45, C:D.45, C:Y.76, C:N.77

1 x NAG- BMA- MAN- NAG: 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

NAG-BMA-MAN-NAG.2: 12 residues within 4Å: Chain A: F.21, F.23, K.26, T.40, V.42, V.44, R.81 Ligands: NAG-FUC.1, NAG-FUC.1, MAN-NAG.3, MAN-NAG.3, MAN.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.26, A:K.26, A:R.81

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

MAN-NAG.3: 3 residues within 4Å: Chain A: F.21 Ligands: NAG-BMA-MAN-NAG.2, NAG.8 No protein-ligand interaction detected (PLIP) MAN-NAG.6: 5 residues within 4Å: Chain C: F.23, T.40, R.81 Ligands: NAG-BMA-MAN-MAN.5, NAG-BMA-MAN-MAN.5 1 PLIP interactions: 1 interactions with chain C Water bridges: C:P.24, C:T.40, C:T.40 Hydrogen bonds: C:R.81

1 x NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-BMA-MAN-MAN.5: 7 residues within 4Å: Chain C: F.21, F.23, V.44, R.81 Ligands: NAG-FUC.4, NAG-FUC.4, MAN-NAG.6 1 PLIP interactions: 1 interactions with chain C Water bridges: C:L.22

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)(Non-functional Binders)

NAG.7: 7 residues within 4Å: Chain B: V.44, D.45, Q.75, N.77, R.81 Ligands: NAG.8, FUC.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.45, B:D.45, B:Q.75, B:N.77 NAG.8: 9 residues within 4Å: Chain B: F.21, V.42, V.44, R.81 Ligands: MAN-NAG.3, NAG.7, BMA.9, MAN.11, FUC.14 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain B: F.23, K.26, T.40 Ligands: MAN.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.26, B:K.26, B:T.40, B:T.40 NAG.13: 1 residues within 4Å: Ligands: MAN.10 No protein-ligand interaction detected (PLIP)

1 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.9: 5 residues within 4Å: Chain B: F.21, F.23 Ligands: NAG.8, MAN.10, MAN.11 No protein-ligand interaction detected (PLIP)

2 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.10: 4 residues within 4Å: Chain B: F.21 Ligands: NAG-BMA-MAN-NAG.2, BMA.9, NAG.13 No protein-ligand interaction detected (PLIP) MAN.11: 4 residues within 4Å: Chain B: F.23 Ligands: NAG.8, BMA.9, NAG.12 No protein-ligand interaction detected (PLIP)

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.14: 5 residues within 4Å: Chain B: Q.75, Y.76, N.77 Ligands: NAG.7, NAG.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.76 Hydrogen bonds: B:Q.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brinkhaus, M. et al., The Fab region of IgG impairs the internalization pathway of FcRn upon Fc engagement. Nat Commun (2022)

Release Date

2022-09-28

Peptides

IgG1-Fc-MST-HN: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

IgG1-Fc-MST-HN

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