› 4dkt

X-ray diffraction
2.98Å resolution

Crystal structure of human peptidylarginine deiminase 4 in complex with N-acetyl-L-threonyl-L-alpha-aspartyl-N5-[(1E)-2-fluoroethanimidoyl]-L-ornithinamide

Released:
DOI: 10.2210/pdb4dkt/pdb
PDB entry 4dkt coloured by chain, front view.
PDB entry 4dkt coloured by chain, side view.
PDB entry 4dkt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Synthesis and screening of a haloacetamidine containing library to identify PAD4 selective inhibitors.
Jones JE, Slack JL, Fang P, Zhang X, Subramanian V, Causey CP, Coonrod SA, Guo M, Thompson PR
ACS Chem Biol 7 160-5 (2012)
PMID: 22004374

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 analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164394 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein-arginine deiminase type-4 Chain: A
Molecule details ›
Chain: A
Length: 668 amino acids
Theoretical weight: 74.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UM07 (Residues: 1-663; Coverage: 100%)
Gene names: PAD4, PADI4, PADI5, PDI5
Sequence domains:
Structure domains:
Thr-Asp-F-amidine Chain: B
Molecule details ›
Chain: B
Length: 5 amino acids
Theoretical weight: 431 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 5 x CA
Ligand SO4 2 x SO4
Ligand EDO 2 x EDO
1 modified residue:
Ligand FIO 1 x FIO

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: C2
Unit cell:
a: 147.654Å b: 61.079Å c: 115.382Å
α: 90° β: 124.54° γ: 90°
R-values:
R R work R free
0.192 0.19 0.23
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

21 review citations

Peptidylarginine deiminases in citrullination, gene regulation, health and pathogenesis.
Wang et al. (2013)
20 more

6 mentions without citation

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