› 7q5w

X-ray diffraction
2.2Å resolution

The tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM peptide

Released:
DOI: 10.2210/pdb7q5w/pdb
PDB entry 7q5w coloured by chain, front view.
PDB entry 7q5w coloured by chain, side view.
PDB entry 7q5w coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The mechanism of allosteric activation of SYK kinase derived from multiple phospho-ITAM-bound structures.
Bradshaw WJ, Harris G, Gileadi O, Katis VL
Structure 32 2337-2351.e4 (2024)
PMID: 39442513

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129163 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Tyrosine-protein kinase SYK Chains: AAA, BBB, CCC, DDD, EEE, FFF
Molecule details ›
Chains: AAA, BBB, CCC, DDD, EEE, FFF
Length: 265 amino acids
Theoretical weight: 29.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P43405 (Residues: 6-269; Coverage: 42%)
Gene name: SYK
Sequence domains: SH2 domain
TYRO protein tyrosine kinase-binding protein Chains: GGG, HHH, III, JJJ, KKK, LLL
Molecule details ›
Chains: GGG, HHH, III, JJJ, KKK, LLL
Length: 20 amino acids
Theoretical weight: 2.49 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: O43914 (Residues: 88-107; Coverage: 22%)
Gene names: DAP12, KARAP, TYROBP

Ligands and Environments

4 bound ligands:
Ligand PO4 6 x PO4
Ligand EDO 3 x EDO
Ligand PEG 1 x PEG
Ligand P4G 1 x P4G
1 modified residue:
Ligand PTR 12 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 117.949Å b: 131.928Å c: 141.526Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.234 0.266
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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