› 2h9g

X-ray diffraction
2.32Å resolution

Crystal structure of phage derived Fab BdF1 with human Death Receptor 5 (DR5)

Released:
DOI: 10.2210/pdb2h9g/pdb
PDB entry 2h9g coloured by chain, front view.
PDB entry 2h9g coloured by chain, side view.
PDB entry 2h9g coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Activation of the proapoptotic death receptor DR5 by oligomeric peptide and antibody agonists.
Li B, Russell SJ, Compaan DM, Totpal K, Marsters SA, Ashkenazi A, Cochran AG, Hymowitz SG, Sidhu SS
J Mol Biol 361 522-36 (2006)
PMID: 16859704

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208026 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Fab BdF1, light chain Chains: A, L
Molecule details ›
Chains: A, L
Length: 214 amino acids
Theoretical weight: 23.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Fab BdF1, heavy chain Chains: B, H
Molecule details ›
Chains: B, H
Length: 228 amino acids
Theoretical weight: 24.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Tumor necrosis factor receptor superfamily member 10B Chains: R, S
Molecule details ›
Chains: R, S
Length: 130 amino acids
Theoretical weight: 14.58 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O14763 (Residues: 54-183; Coverage: 33%)
Gene names: DR5, KILLER, TNFRSF10B, TRAILR2, TRICK2, UNQ160/PRO186, ZTNFR9
Sequence domains: TNFR/NGFR cysteine-rich region
Structure domains: Tumor Necrosis Factor Receptor, subunit A, domain 2

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P21
Unit cell:
a: 99.814Å b: 61.389Å c: 108.269Å
α: 90° β: 101.17° γ: 90°
R-values:
R R work R free
0.234 0.228 0.282
Expression systems:
  • Escherichia coli
  • Spodoptera frugiperda

Quick links

Citations

7 review citations

The promise and challenges of immune agonist antibody development in cancer.
Mayes et al. (2018)
6 more

7 mentions without citation

Architecture of Eph receptor clusters.
Himanen et al. (2010)
6 more