› 6r3k

X-ray diffraction
2.2Å resolution

Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor

Released:
DOI: 10.2210/pdb6r3k/pdb
PDB entry 6r3k coloured by chain, front view.
PDB entry 6r3k coloured by chain, side view.
PDB entry 6r3k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Terphenyl-Based Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Protein-Protein Interaction.
Muszak D, Surmiak E, Plewka J, Magiera-Mularz K, Kocik-Krol J, Musielak B, Sala D, Kitel R, Stec M, Weglarczyk K, Siedlar M, Dömling A, Skalniak L, Holak TA
J Med Chem 64 11614-11636 (2021)
PMID: 34313116

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192784 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Programmed cell death 1 ligand 1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 128 amino acids
Theoretical weight: 14.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NZQ7 (Residues: 18-134; Coverage: 43%)
Gene names: B7H1, CD274, PDCD1L1, PDCD1LG1, PDL1
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments

2 bound ligands:
Ligand EDO 2 x EDO
Ligand JQT 2 x JQT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P212121
Unit cell:
a: 40.527Å b: 84.609Å c: 164.116Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.214 0.259
Expression system: Escherichia coli

Quick links

Citations

4 review citations

PD-1/PD-L1 and DNA Damage Response in Cancer.
Kciuk et al. (2023)
3 more

21 mentions without citation

Computational Approaches Drive Developments in Immune-Oncology Therapies for PD-1/PD-L1 Immune Checkpoint Inhibitors.
Sobral et al. (2023)
20 more