› 5nal

X-ray diffraction
2.2Å resolution

The crystal structure of inhibitor-15 covalently bound to PDE6D

Released:
DOI: 10.2210/pdb5nal/pdb
Model geometry
Fit model/data
PDB entry 5nal coloured by chain, front view.
PDB entry 5nal coloured by chain, side view.
PDB entry 5nal coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Covalent Protein Labeling at Glutamic Acids.
Martín-Gago P, Fansa EK, Winzker M, Murarka S, Janning P, Schultz-Fademrecht C, Baumann M, Wittinghofer A, Waldmann H
Cell Chem Biol 24 589-597.e5 (2017)
PMID: 28434875

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129171 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta Chain: B
Molecule details ›
Chain: B
Length: 150 amino acids
Theoretical weight: 17.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43924 (Residues: 1-150; Coverage: 100%)
Gene names: PDE6D, PDED
Sequence domains: GMP-PDE, delta subunit
Structure domains: GMP phosphodiesterase, delta subunit

Ligands and Environments

1 bound ligand:
Ligand 8RQ 1 x 8RQ
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ENRAF-NONIUS FR571
Spacegroup: P3221
Unit cell:
a: 56.07Å b: 56.07Å c: 115.08Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.198 0.195 0.244
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications.
Liu et al. (2020)
5 more

1 mention without citation

Validation of a small molecule inhibitor of PDE6D-RAS interaction with favorable anti-leukemic effects.
Canovas Nunes et al. (2022)