9DKP: PDB entry 9DKP

The structure of human vacuolar protein sorting 34 catalytic domain bound to RD-I-53. Determined by X-ray diffraction at 2.16 Å resolution. Released 17 Sept 2025.

Method

X-ray diffraction

Resolution

2.16 Å

Organism

Homo sapiens

Chains

1

Atoms

4,274

Mol. weight

69.3 kDa

Ligands

ETZ, A1A6F, ETX

Released

17 Sept 2025

Explore 9DKP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DKP contains 34 α-helices and 12 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 34 helices, 12 β-strands

Molecules and chains

>9DKP_1 Phosphatidylinositol 3-kinase catalytic subunit type 3 (chains B)
MGHHHHHHHHHHAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCV
NWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLL
QLVQALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPP
PASKTKEVPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMY
LNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALL
GDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKH
GDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTE
GSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKL
FHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLIL
NLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALF

Ligands and cofactors

Water and common crystallization additives (DMS, K, CL) are not listed.

Primary citation

Facile Bacterial Production of Human Vacuolar Protein Sorting 34 Enables Structural Characterization of Novel Inhibitors. Abiodun, W.O., Dass, R., Tsubaki, E. et al. To be published.

Related structures

Other PDB entries of the same protein (UniProt Q8NEB9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 6HOG 1.26 Å, Structure of VPS34 LIR motif bound to GABARAP
• 7RSP 1.67 Å, Structure of the VPS34 kinase domain with compound 14
• 7RSV 1.78 Å, Structure of the VPS34 kinase domain with compound 5
• 7RSJ 1.88 Å, Structure of the VPS34 kinase domain with compound 14
• 4UWH 1.93 Å, Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-yl)-1-(3-methyl-2-oxo-…
• 9NIN 2.01 Å, The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-I-86
• 8RXR 2.06 Å, Crystal structure of VPS34 in complex with inhibitor SB02024
• 9ORM 2.06 Å, The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-I-137
• 6I3U 2.09 Å, Optimization of potent and selective ATM inhibitors suitable for a proof-of-concept…
• 9ZF4 2.09 Å, The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-83
• 3LS8 2.25 Å, Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimi…
• 6HOH 2.25 Å, Structure of VPS34 LIR motif (S249E) bound to GABARAP

Browse structure collections

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