› 4k9e

X-ray diffraction
2.7Å resolution

Crystal structure of KIT D4D5 fragment in complex with anti-Kit antibodies Fab79D

Released:
DOI: 10.2210/pdb4k9e/pdb
PDB entry 4k9e coloured by chain, front view.
PDB entry 4k9e coloured by chain, side view.
PDB entry 4k9e coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for KIT receptor tyrosine kinase inhibition by antibodies targeting the D4 membrane-proximal region.
Reshetnyak AV, Nelson B, Shi X, Boggon TJ, Pavlenco A, Mandel-Bausch EM, Tome F, Suzuki Y, Sidhu SS, Lax I, Schlessinger J
Proc Natl Acad Sci U S A 110 17832-7 (2013)
PMID: 24127596

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
  • not assigned
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-210490 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
light chain Chain: L
Molecule details ›
Chain: L
Length: 228 amino acids
Theoretical weight: 24.94 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Structure domains: Immunoglobulins
heavy chain Chain: H
Molecule details ›
Chain: H
Length: 221 amino acids
Theoretical weight: 23.54 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Mast/stem cell growth factor receptor Kit Chain: C
Molecule details ›
Chain: C
Length: 214 amino acids
Theoretical weight: 24.04 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: P10721 (Residues: 308-518; Coverage: 22%)
Gene names: KIT, SCFR
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P6522
Unit cell:
a: 94.577Å b: 94.577Å c: 320.876Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.248 0.247 0.282
Expression systems:
  • Escherichia coli
  • unidentified baculovirus

Quick links

Citations

2 review citations

Targeting KIT on innate immune cells to enhance the antitumor activity of checkpoint inhibitors.
Stahl et al. (2016)
1 more

1 mention without citation

Structural basis for KIT receptor tyrosine kinase inhibition by antibodies targeting the D4 membrane-proximal region.
Reshetnyak et al. (2013)