› 5l6o

X-ray diffraction
1.88Å resolution

EphB3 kinase domain covalently bound to an irreversible inhibitor (compound 3)

Released:
DOI: 10.2210/pdb5l6o/pdb
PDB entry 5l6o coloured by chain, front view.
PDB entry 5l6o coloured by chain, side view.
PDB entry 5l6o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Development of Specific, Irreversible Inhibitors for a Receptor Tyrosine Kinase EphB3.
Kung A, Chen YC, Schimpl M, Ni F, Zhu J, Turner M, Molina H, Overman R, Zhang C
J Am Chem Soc 138 10554-60 (2016)
PMID: 27478969

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157088 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ephrin type-B receptor 3 Chain: A
Molecule details ›
Chain: A
Length: 298 amino acids
Theoretical weight: 33.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P54753 (Residues: 616-910; Coverage: 31%)
Gene names: EPHB3, ETK2, HEK2, TYRO6
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand 6P6 1 x 6P6
Ligand DIO 1 x DIO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 46.817Å b: 57.214Å c: 113.184Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.189 0.206
Expression system: Escherichia coli

Quick links

Citations

4 review citations

The Cysteinome of Protein Kinases as a Target in Drug Development.
Chaikuad et al. (2018)
3 more