› 8q1x

X-ray diffraction
1.85Å resolution

Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation

Released:
DOI: 10.2210/pdb8q1x/pdb
PDB entry 8q1x coloured by chain, front view.
PDB entry 8q1x coloured by chain, side view.
PDB entry 8q1x coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation.
Roske Y, Cappel C, Cremer N, Hoffmann P, Koudelka T, Tholey A, Heinemann U, Daumke O, Damme M
Nucleic Acids Res (2023)
PMID: 37994783

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236367 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
5'-3' exonuclease PLD3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 433 amino acids
Theoretical weight: 48.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IV08 (Residues: 61-490; Coverage: 88%)
Gene name: PLD3
Sequence domains: PLD-like domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
6 bound ligands:
Ligand PST 4 x PST
Ligand PO4 3 x PO4
Ligand EDO 15 x EDO
Ligand MN 2 x MN
Ligand SO4 4 x SO4
Ligand MG 2 x MG
1 modified residue:
Ligand OCS 2 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P21
Unit cell:
a: 60.535Å b: 115.452Å c: 101.335Å
α: 90° β: 106.62° γ: 90°
R-values:
R R work R free
0.174 0.174 0.199
Expression system: Escherichia coli

Quick links

Citations

1 mention without citation

Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation.
Roske et al. (2024)