› 5anl

X-ray diffraction
2.7Å resolution

Crystal structure of VPS34 in complex with (2S)-8-((3R)-3- Methylmorpholin-4-yl)-1-(3-methyl-2-oxo- butyl)-2-(trifluoromethyl)-3, 4-dihydro-2H-pyrimido(1,2-a)pyrimidin-6- one, processed with the CrystalDirect automated mounting and cryo-cooling technology

Released:
DOI: 10.2210/pdb5anl/pdb
PDB entry 5anl coloured by chain, front view.
PDB entry 5anl coloured by chain, side view.
PDB entry 5anl coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Automated harvesting and processing of protein crystals through laser photoablation.
Zander U, Hoffmann G, Cornaciu I, Marquette JP, Papp G, Landret C, Seroul G, Sinoir J, Röwer M, Felisaz F, Rodriguez-Puente S, Mariaule V, Murphy P, Mathieu M, Cipriani F, Márquez JA
OpenAccess logo Acta Crystallogr D Struct Biol 72 454-66 (2016)
PMID: 27050125

Function and Biology Details

Reaction catalysed: 
ATP + 1-phosphatidyl-1D-myo-inositol = ADP + 1-phosphatidyl-1D-myo-inositol 3-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-185509 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphatidylinositol 3-kinase catalytic subunit type 3 Chain: A
Molecule details ›
Chain: A
Length: 601 amino acids
Theoretical weight: 68.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8NEB9 (Residues: 282-879; Coverage: 67%)
Gene names: PIK3C3, VPS34
Sequence domains:
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P21212
Unit cell:
a: 88.215Å b: 145.763Å c: 61.474Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.205 0.267
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Protein X-ray Crystallography and Drug Discovery.
Maveyraud et al. (2020)
1 more

2 mentions without citation

Advances in chemical proteomic evaluation of lipid kinases-DAG kinases as a case study.
Ware et al. (2021)
1 more