› 6ohs

X-ray diffraction
3.2Å resolution

Structure of compound 3 (ML299) bound human Phospholipase D2 catalytic domain

Released:
DOI: 10.2210/pdb6ohs/pdb
PDB entry 6ohs coloured by chain, front view.
PDB entry 6ohs coloured by chain, side view.
PDB entry 6ohs coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Human PLD structures enable drug design and characterization of isoenzyme selectivity.
Metrick CM, Peterson EA, Santoro JC, Enyedy IJ, Murugan P, Chen T, Michelsen K, Cullivan M, Spilker KA, Kumar PR, May-Dracka TL, Chodaparambil JV
Nat Chem Biol 16 391-399 (2020)
PMID: 32042197

Function and Biology Details

Reaction catalysed: 
A phosphatidylcholine + H(2)O = choline + a phosphatidate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127215 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phospholipase D2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 640 amino acids
Theoretical weight: 72.85 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O14939 (Residues: 294-933; Coverage: 69%)
Gene name: PLD2
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand MJY 4 x MJY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 89.06Å b: 132.317Å c: 114.611Å
α: 90° β: 100.01° γ: 90°
R-values:
R R work R free
0.28 0.278 0.319
Expression system: Trichoplusia ni

Quick links

Citations

1 review citation

Structure and regulation of human phospholipase D.
Bowling et al. (2021)
10 other articles

1 mention without citation

Crystal Structure of a Phospholipase D from the Plant-Associated Bacteria Serratia plymuthica Strain AS9 Reveals a Unique Arrangement of Catalytic Pocket.
Wang et al. (2021)