SMTL ID : 8as0.7 (7 other biounits)

PD-1 extracellular domain in complex with Fab fragment from D12 antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG-BMA-MAN.1: 3 residues within 4Å: Chain C: E.23, R.91, N.93 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.2: 4 residues within 4Å: Chain C: N.26, R.73, S.86, V.88 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:N.26 Hydrogen bonds: C:N.26, C:T.75, C:S.86, C:S.86

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 7 residues within 4Å: Chain C: N.35, T.36, S.37, E.38, F.40, P.60, Q.76 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.38, C:E.38, C:Q.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peissert, F. et al., Selection of a PD-1 blocking antibody from a novel fully human phage display library. Protein Sci. (2022)

Release Date

2022-11-23

Peptides

D12 antibody light chain, Fab fragment: A
D12 antibody heavy chain, Fab fragment: B
Programmed cell death protein 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
V

B
W

C
X

D12 antibody light chain, Fab fragment

D12 antibody heavy chain, Fab fragment

Programmed cell death protein 1

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