› 6np9

X-ray diffraction
1.27Å resolution

PD-L1 IgV domain V76T with fragment

Released:
DOI: 10.2210/pdb6np9/pdb
PDB entry 6np9 coloured by chain, front view.
PDB entry 6np9 coloured by chain, side view.
PDB entry 6np9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Fragment-based screening of programmed death ligand 1 (PD-L1).
Perry E, Mills JJ, Zhao B, Wang F, Sun Q, Christov PP, Tarr JC, Rietz TA, Olejniczak ET, Lee T, Fesik S
Bioorg Med Chem Lett 29 786-790 (2019)
PMID: 30728114

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 Chain: A
Molecule details ›
Chain: A
Length: 127 amino acids
Theoretical weight: 14.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
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

1 bound ligand:
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2221
Unit cell:
a: 53.331Å b: 54.111Å c: 85.724Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.202 0.218
Expression system: Escherichia coli K-12

Quick links

Citations

6 review citations

Development of the Inhibitors that Target the PD-1/PD-L1 Interaction-A Brief Look at Progress on Small Molecules, Peptides and Macrocycles.
Guzik et al. (2019)
5 more

3 mentions without citation

A Comprehensive Computational Insight into the PD-L1 Binding to PD-1 and Small Molecules.
Fantacuzzi et al. (2024)
2 more