› 3x3f

X-ray diffraction
2.1Å resolution

TRAIL-R2 Extracellular Region Complexed to a Fab fragment from Human Agonist Antibody KMTR2

Released:
DOI: 10.2210/pdb3x3f/pdb
PDB entry 3x3f coloured by chain, front view.
PDB entry 3x3f coloured by chain, side view.
PDB entry 3x3f coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
TRAIL-R2 Superoligomerization Induced by Human Monoclonal Agonistic Antibody KMTR2.
Tamada T, Shinmi D, Ikeda M, Yonezawa Y, Kataoka S, Kuroki R, Mori E, Motoki K
Sci Rep 5 17936 (2015)
PMID: 26672965

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-234980 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Heavy chain of KMTR2 Chain: H
Molecule details ›
Chain: H
Length: 229 amino acids
Theoretical weight: 24.9 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
Structure domains: Immunoglobulins
Light chain of KMTR2 Chain: L
Molecule details ›
Chain: L
Length: 214 amino acids
Theoretical weight: 23.35 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
Structure domains: Immunoglobulins
Tumor necrosis factor receptor superfamily member 10B Chain: A
Molecule details ›
Chain: A
Length: 142 amino acids
Theoretical weight: 15.98 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: O14763 (Residues: 54-184; Coverage: 34%)
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

3 bound ligands:
Ligand NAG 1 x NAG
Ligand CL 1 x CL
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: I222
Unit cell:
a: 144.974Å b: 151.563Å c: 65.044Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.186 0.224
Expression system: Cricetulus griseus

Quick links

Citations

5 review citations

Next generation antibody drugs: pursuit of the 'high-hanging fruit'.
Carter et al. (2018)
4 more

5 mentions without citation

TRAIL-R2 Superoligomerization Induced by Human Monoclonal Agonistic Antibody KMTR2.
Tamada et al. (2015)
4 more