› 1tbf

X-ray diffraction
1.3Å resolution

Catalytic Domain Of Human Phosphodiesterase 5A in Complex with Sildenafil

Released:
DOI: 10.2210/pdb1tbf/pdb
PDB entry 1tbf coloured by chain, front view.
PDB entry 1tbf coloured by chain, side view.
PDB entry 1tbf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A glutamine switch mechanism for nucleotide selectivity by phosphodiesterases.
Zhang KY, Card GL, Suzuki Y, Artis DR, Fong D, Gillette S, Hsieh D, Neiman J, West BL, Zhang C, Milburn MV, Kim SH, Schlessinger J, Bollag G
Mol Cell 15 279-86 (2004)
PMID: 15260978

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131208 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
cGMP-specific 3',5'-cyclic phosphodiesterase Chain: A
Molecule details ›
Chain: A
Length: 347 amino acids
Theoretical weight: 39.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O76074 (Residues: 534-677, 678-858; Coverage: 37%)
Gene names: PDE5, PDE5A
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

4 bound ligands:
Ligand ZN 1 x ZN
Ligand MG 1 x MG
Ligand VIA 1 x VIA
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P3121
Unit cell:
a: 76.097Å b: 76.097Å c: 99.272Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.159 0.157 0.186
Expression system: Escherichia coli

Quick links

Citations

19 review citations

Biochemistry and physiology of cyclic nucleotide phosphodiesterases: essential components in cyclic nucleotide signaling.
Conti et al. (2007)
18 more

15 mentions without citation

Shifting the paradigm in treating multi-factorial diseases: polypharmacological co-inhibitors of HDAC6.
Chan et al. (2021)
14 more