› 4ixu

X-ray diffraction
1.9Å resolution

Crystal structure of human Arginase-2 complexed with inhibitor 11d: {(5R)-5-amino-5-carboxy-5-[(3-endo)-8-(3,4-dichlorobenzyl)-8-azabicyclo[3.2.1]oct-3-yl]pentyl}(trihydroxy)borate(1-)

Released:
DOI: 10.2210/pdb4ixu/pdb
PDB entry 4ixu coloured by chain, front view.
PDB entry 4ixu coloured by chain, side view.
PDB entry 4ixu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Synthesis of quaternary α-amino acid-based arginase inhibitors via the Ugi reaction.
Golebiowski A, Whitehouse D, Beckett RP, Van Zandt M, Ji MK, Ryder TR, Jagdmann E, Andreoli M, Lee Y, Sheeler R, Conway B, Olczak J, Mazur M, Czestkowski W, Piotrowska W, Cousido-Siah A, Ruiz FX, Mitschler A, Podjarny A, Schroeter H
Bioorg Med Chem Lett 23 4837-41 (2013)
PMID: 23886684

Function and Biology Details

Reaction catalysed: 
L-arginine + H(2)O = L-ornithine + urea
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160276 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Arginase-2, mitochondrial Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 306 amino acids
Theoretical weight: 33.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P78540 (Residues: 24-329; Coverage: 86%)
Gene name: ARG2
Sequence domains: Arginase family
Structure domains: Ureohydrolase domain

Ligands and Environments

4 bound ligands:
Ligand MN 6 x MN
Ligand BEN 3 x BEN
Ligand BME 6 x BME
Ligand 38I 3 x 38I
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P42212
Unit cell:
a: 127.4Å b: 127.4Å c: 159.249Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.167 0.193
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Targeting Metalloenzymes for Therapeutic Intervention.
Chen et al. (2019)
4 more

3 mentions without citation

Metformin directly targets the H3K27me3 demethylase KDM6A/UTX.
Cuyàs et al. (2018)
2 more