› 6umt

X-ray diffraction
1.99Å resolution

High-affinity human PD-1 PD-L2 complex

Released:
DOI: 10.2210/pdb6umt/pdb
PDB entry 6umt coloured by chain, front view.
PDB entry 6umt coloured by chain, side view.
PDB entry 6umt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery.
Tang S, Kim PS
Proc Natl Acad Sci U S A 116 24500-24506 (2019)
PMID: 31727844

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172198 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Programmed cell death protein 1 Chain: A
Molecule details ›
Chain: A
Length: 140 amino acids
Theoretical weight: 15.43 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q15116 (Residues: 33-150; Coverage: 45%)
Gene names: PD1, PDCD1
Sequence domains: Immunoglobulin V-set domain
Programmed cell death 1 ligand 2 Chain: B
Molecule details ›
Chain: B
Length: 123 amino acids
Theoretical weight: 13.95 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9BQ51 (Residues: 1-123; Coverage: 41%)
Gene names: B7DC, CD273, PDCD1L2, PDCD1LG2, PDL2

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P212121
Unit cell:
a: 41.291Å b: 67.798Å c: 89.701Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.198 0.226
Expression system: Homo sapiens

Quick links

Citations

5 review citations

Immunotherapy in Treating EGFR-Mutant Lung Cancer: Current Challenges and New Strategies.
To et al. (2021)
4 more

3 mentions without citation

A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery.
Tang et al. (2019)
2 more