PDBe 5jxe

X-ray diffraction
2.9Å resolution

Human PD-1 ectodomain complexed with Pembrolizumab Fab

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Programmed cell death protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 114 amino acids
Theoretical weight: 12.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15116 (Residues: 33-146; Coverage: 43%)
Gene names: PD1, PDCD1
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins
Pembrolizumab Fab light chain Chains: C, F
Molecule details ›
Chains: C, F
Length: 218 amino acids
Theoretical weight: 23.77 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Pembrolizumab Fab heavy chain Chains: D, G
Molecule details ›
Chains: D, G
Length: 218 amino acids
Theoretical weight: 23.68 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-1
Spacegroup: P6522
Unit cell:
a: 105.554Å b: 105.554Å c: 380.048Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.262 0.261 0.286
Expression systems:
  • Escherichia coli
  • Homo sapiens