› 5sym

X-ray diffraction
1.55Å resolution

Cocrystal structure of the human acyl protein thioesterase 1 with an isoform-selective inhibitor, ML348

Released:
DOI: 10.2210/pdb5sym/pdb
PDB entry 5sym coloured by chain, front view.
PDB entry 5sym coloured by chain, side view.
PDB entry 5sym coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2).
Won SJ, Davda D, Labby KJ, Hwang SY, Pricer R, Majmudar JD, Armacost KA, Rodriguez LA, Rodriguez CL, Chong FS, Torossian KA, Palakurthi J, Hur ES, Meagher JL, Brooks CL, Stuckey JA, Martin BR
ACS Chem Biol 11 3374-3382 (2016)
PMID: 27748579

Function and Biology Details

Reaction catalysed: 
Palmitoyl-[protein] + H(2)O = palmitate + [protein]
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131082 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Acyl-protein thioesterase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 230 amino acids
Theoretical weight: 24.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75608 (Residues: 1-230; Coverage: 100%)
Gene names: APT1, LPL1, LYPLA1
Sequence domains: Phospholipase/Carboxylesterase
Structure domains: alpha/beta hydrolase

Ligands and Environments

3 bound ligands:
Ligand 71Q 2 x 71Q
Ligand EDO 7 x EDO
Ligand CL 4 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Unit cell:
a: 71.67Å b: 73.69Å c: 81.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.179 0.199
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Protein Lipidation in Cell Signaling and Diseases: Function, Regulation, and Therapeutic Opportunities.
Chen et al. (2018)
10 more

12 mentions without citation

Protein depalmitoylases.
Won et al. (2018)
11 more