5ggr

X-ray diffraction
3.3Å resolution

PD-1 in complex with nivolumab Fab

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-212030 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
heavy chain Chains: A, H
Molecule details ›
Chains: A, H
Length: 225 amino acids
Theoretical weight: 24.28 KDa
Source organism: Homo sapiens
Expression system: Not provided
Structure domains: Immunoglobulins
light chain Chains: B, L
Molecule details ›
Chains: B, L
Length: 214 amino acids
Theoretical weight: 23.4 KDa
Source organism: Homo sapiens
Expression system: Not provided
Structure domains: Immunoglobulins
Programmed cell death protein 1 Chains: Y, Z
Molecule details ›
Chains: Y, Z
Length: 125 amino acids
Theoretical weight: 14.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
UniProt:
  • Canonical: Q15116 (Residues: 26-150; Coverage: 47%)
Gene names: PD1, PDCD1
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: P21
Unit cell:
a: 91.29Å b: 48.612Å c: 134.904Å
α: 90° β: 102.12° γ: 90°
R-values:
R R work R free
0.224 0.222 0.268
Expression systems:
  • Not provided
  • Escherichia coli-Pichia pastoris shuttle vector pPpARG4