› 8v5t

X-ray diffraction
2.3Å resolution

Crystal structure of Alzheimers disease phospholipase D3

Released:
DOI: 10.2210/pdb8v5t/pdb
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PDB entry 8v5t coloured by chain, front view.
PDB entry 8v5t coloured by chain, side view.
PDB entry 8v5t coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of Alzheimer's disease phospholipase D3 provides a molecular basis for understanding its normal and pathological functions.
Ishii K, Hermans SJ, Georgopoulou ME, Nero TL, Hancock NC, Crespi GAN, Gorman MA, Gooi JH, Parker MW
FEBS J (2024)
PMID: 39325669

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-275131 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
5'-3' exonuclease PLD3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 490 amino acids
Theoretical weight: 54.76 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8IV08 (Residues: 1-490; Coverage: 100%)
Gene name: PLD3
Sequence domains: PLD-like domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand SO4 10 x SO4
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: C2
Unit cell:
a: 205.137Å b: 60.566Å c: 111.501Å
α: 90° β: 98.72° γ: 90°
R-values:
R R work R free
0.186 0.185 0.209
Expression system: Homo sapiens

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