› 4od2

X-ray diffraction
3.2Å resolution

Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5

Released:
DOI: 10.2210/pdb4od2/pdb
PDB entry 4od2 coloured by chain, front view.
PDB entry 4od2 coloured by chain, side view.
PDB entry 4od2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and functional analysis of the interaction between the agonistic monoclonal antibody Apomab and the proapoptotic receptor DR5.
Adams C, Totpal K, Lawrence D, Marsters S, Pitti R, Yee S, Ross S, Deforge L, Koeppen H, Sagolla M, Compaan D, Lowman H, Hymowitz S, Ashkenazi A
Cell Death Differ 15 751-61 (2008)
PMID: 18219321

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-518132 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Fab fragment of drozitumab, light chain Chain: A
Molecule details ›
Chain: A
Length: 213 amino acids
Theoretical weight: 22.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Fab fragment of drozitumab, heavy chain Chain: B
Molecule details ›
Chain: B
Length: 232 amino acids
Theoretical weight: 24.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Tumor necrosis factor receptor superfamily member 10B Chain: S
Molecule details ›
Chain: S
Length: 111 amino acids
Theoretical weight: 12.49 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O14763 (Residues: 73-183; Coverage: 29%)
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 5.0.2
Spacegroup: P6
Unit cell:
a: 128.317Å b: 128.317Å c: 68.386Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.248 0.241 0.305
Expression systems:
  • Escherichia coli
  • Spodoptera frugiperda

Quick links

Citations

29 review citations

Directing cancer cells to self-destruct with pro-apoptotic receptor agonists.
Ashkenazi A. (2008)
28 more

4 mentions without citation

Current Challenges and Opportunities in Designing Protein-Protein Interaction Targeted Drugs.
Shin et al. (2020)
3 more