› 5ml2

X-ray diffraction
1.6Å resolution

The crystal structure of PDE6D in complex with inhibitor-3

Released:
DOI: 10.2210/pdb5ml2/pdb
PDB entry 5ml2 coloured by chain, front view.
PDB entry 5ml2 coloured by chain, side view.
PDB entry 5ml2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A PDE6δ-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2.
Martín-Gago P, Fansa EK, Klein CH, Murarka S, Janning P, Schürmann M, Metz M, Ismail S, Schultz-Fademrecht C, Baumann M, Bastiaens PI, Wittinghofer A, Waldmann H
Angew Chem Int Ed Engl 56 2423-2428 (2017)
PMID: 28106325

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: 149 amino acids
Theoretical weight: 17.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43924 (Residues: 2-150; Coverage: 99%)
Gene names: PDE6D, PDED
Sequence domains: GMP-PDE, delta subunit
Structure domains: GMP phosphodiesterase, delta subunit

Ligands and Environments

1 bound ligand:
Ligand NH6 1 x NH6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P3221
Unit cell:
a: 55.65Å b: 55.65Å c: 115.34Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.202 0.227
Expression system: Escherichia coli

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Citations

25 review citations

Recent advances in the development of protein-protein interactions modulators: mechanisms and clinical trials.
Lu et al. (2020)
24 more