› 3bik

X-ray diffraction
2.65Å resolution

Crystal Structure of the PD-1/PD-L1 Complex

Released:
DOI: 10.2210/pdb3bik/pdb
PDB entry 3bik coloured by chain, front view.
PDB entry 3bik coloured by chain, side view.
PDB entry 3bik coloured by chain, top view.
Source organisms:
Primary publication:
The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors.
Lin DY, Tanaka Y, Iwasaki M, Gittis AG, Su HP, Mikami B, Okazaki T, Honjo T, Minato N, Garboczi DN
Proc Natl Acad Sci U S A 105 3011-6 (2008)
PMID: 18287011

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-169696 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Programmed cell death 1 ligand 1 Chain: A
Molecule details ›
Chain: A
Length: 222 amino acids
Theoretical weight: 25.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NZQ7 (Residues: 18-239; Coverage: 81%)
Gene names: B7H1, CD274, PDCD1L1, PDCD1LG1, PDL1
Sequence domains:
Structure domains: Immunoglobulins
Programmed cell death protein 1 Chains: B, C
Molecule details ›
Chains: B, C
Length: 134 amino acids
Theoretical weight: 15.09 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q02242 (Residues: 25-157; Coverage: 50%)
Gene names: Pd1, Pdcd1
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: P212121
Unit cell:
a: 56.46Å b: 63.94Å c: 159.92Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.211 0.268
Expression system: Escherichia coli

Quick links

Citations

55 review citations

Molecular mechanisms of T cell co-stimulation and co-inhibition.
Chen et al. (2013)
54 more

48 mentions without citation

Human cancer immunotherapy with antibodies to the PD-1 and PD-L1 pathway.
Ohaegbulam et al. (2015)
47 more