› 5lbo

X-ray diffraction
2.25Å resolution

Function and Biology Details

Reaction catalysed: 
Adenosine 3',5'-cyclic phosphate + H(2)O = adenosine 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170654 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3',5'-cyclic-AMP phosphodiesterase 4D Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 364 amino acids
Theoretical weight: 41.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08499 (Residues: 381-740; Coverage: 45%)
Gene names: DPDE3, PDE4D
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

7 bound ligands:
Ligand ZN 4 x ZN
Ligand MG 4 x MG
Ligand EDO 28 x EDO
Ligand DTT 3 x DTT
Ligand 6M5 4 x 6M5
Ligand EPE 2 x EPE
Ligand PEG 2 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 98.223Å b: 111.092Å c: 160.798Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.174 0.21
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Current Treatments to Control African Trypanosomiasis and One Health Perspective.
Venturelli et al. (2022)
10 other articles

1 mention without citation

Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity.
Blaazer et al. (2018)