SMTL ID : 6jbt.1

Complex structure of toripalimab-Fab and PD-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 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.1: 5 residues within 4Å: Chain A: N.30, R.77, S.90, V.92, R.93 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.2: 6 residues within 4Å: Chain A: N.39, T.40, S.41, E.42, F.44, P.64 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.44, A:P.64

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 2 residues within 4Å: Chain A: R.95, N.97 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., Glycosylation-independent binding of monoclonal antibody toripalimab to FG loop of PD-1 for tumor immune checkpoint therapy. Mabs (2019)

Release Date

2019-06-19

Peptides

Programmed cell death protein 1: A
Heavy chain: B
Light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
H

C
L

Programmed cell death protein 1

Heavy chain

Light chain