› 2dw5

X-ray diffraction
2.3Å resolution

Crystal structure of human peptidylarginine deiminase 4 in complex with N-alpha-benzoyl-N5-(2-fluoro-1-iminoethyl)-L-ornithine amide

Released:
DOI: 10.2210/pdb2dw5/pdb
PDB entry 2dw5 coloured by chain, front view.
PDB entry 2dw5 coloured by chain, side view.
PDB entry 2dw5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Inhibitors and inactivators of protein arginine deiminase 4: functional and structural characterization.
Luo Y, Arita K, Bhatia M, Knuckley B, Lee YH, Stallcup MR, Sato M, Thompson PR
Biochemistry 45 11727-36 (2006)
PMID: 17002273

Function and Biology Details

Reaction catalysed: 
Protein L-arginine + H(2)O = protein L-citrulline + NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193952 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protein-arginine deiminase type-4 Chain: A
Molecule details ›
Chain: A
Length: 671 amino acids
Theoretical weight: 74.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UM07 (Residues: 1-663; Coverage: 100%)
Gene names: PAD4, PADI4, PADI5, PDI5
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand CA 5 x CA
Ligand SO4 3 x SO4
Ligand BFB 1 x BFB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2
Unit cell:
a: 146.259Å b: 60.516Å c: 114.911Å
α: 90° β: 124.19° γ: 90°
R-values:
R R work R free
0.2 0.198 0.252
Expression system: Escherichia coli BL21(DE3)

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Citations

46 review citations

Regulation of histone methylation by demethylimination and demethylation.
Klose et al. (2007)
45 more

11 mentions without citation

Chemical biology of protein arginine modifications in epigenetic regulation.
Fuhrmann et al. (2015)
10 more