9dkp

The structure of human vacuolar protein sorting 34 catalytic domain bound to RD-I-53

Method: X-RAY DIFFRACTION D_max: 82.5 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Phosphatidylinositol 3-kinase catalytic subunit type 3

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 290–871	Not recorded	A1A6F (8R)-3-(1,3-benzothiazol-2-yl)pyrazolo[1,5-a]pyrimidine × 1 ETX 2-ETHOXYETHANOL × 1 ETZ diethyl ether × 2 DMS DIMETHYL SULFOXIDE × 1 K POTASSIUM ION × 2 CL CHLORIDE ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；298 K；20% PEG, 0.2M MES pH 6.0	Resolution 2.16 Å R-free 0.235

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9DKP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11MM The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-81 Deposited 2026-03-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 290–871（582 aa）	Not recorded	GOL GLYCEROL × 2 A1C9V (8S)-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]pyrazolo[1,5-a]pyrimidine × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol monomethyl ether 5,000	Resolution 2.69 Å R-free 0.265
11YC The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-123 Deposited 2026-03-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 290–871（582 aa）	Not recorded	A1DAY (8S)-3-(6-butyl-1,3-benzothiazol-2-yl)pyrazolo[1,5-a]pyrimidine × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；Ammonium Acetate, HEPES, Polyethylene glycol 3,350	Resolution 2.41 Å R-free 0.220
13BV Cryo-EM structure of human PI3KC3-C1 complex Deposited 2026-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–887（887 aa）	Not recorded	MYR MYRISTIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.77 Å
3IHY Human PIK3C3 crystal structure Deposited 2009-07-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–879（598 aa） Fragment：UNP residues 282-879	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M ammonium acetate 25% PEG3350 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.255
3IHY Human PIK3C3 crystal structure Deposited 2009-07-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 282–879（598 aa） Fragment：UNP residues 282-879	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M ammonium acetate 25% PEG3350 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.255
3IHY Human PIK3C3 crystal structure Deposited 2009-07-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 282–879（598 aa） Fragment：UNP residues 282-879	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M ammonium acetate 25% PEG3350 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.255
3IHY Human PIK3C3 crystal structure Deposited 2009-07-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 282–879（598 aa） Fragment：UNP residues 282-879	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M ammonium acetate 25% PEG3350 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.255
3IHY Human PIK3C3 crystal structure Deposited 2009-07-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 282–879（598 aa） Fragment：UNP residues 282-879	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M ammonium acetate 25% PEG3350 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.255
3LS8 Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-phenol Deposited 2010-02-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 268–879（612 aa） Fragment：UNP Residues 268-879	Not recorded	AJZ 3-(4-morpholin-4-ylthieno[3,2-d]pyrimidin-2-yl)phenol × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG3350, 0.2M ammonium acetate, 0.1M hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.25 Å R-free 0.251
3LS8 Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-phenol Deposited 2010-02-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 268–879（612 aa） Fragment：UNP Residues 268-879	Not recorded	AJZ 3-(4-morpholin-4-ylthieno[3,2-d]pyrimidin-2-yl)phenol × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG3350, 0.2M ammonium acetate, 0.1M hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.25 Å R-free 0.251
4OYS CRYSTAL STRUCTURE OF VPS34 IN COMPLEX WITH SAR405. Deposited 2014-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–879（598 aa） Fragment：UNP residues 282-879	Not recorded	SO4 SULFATE ION × 4 1TT (8S)-9-[(5-chloranylpyridin-3-yl)methyl]-2-[(3R)-3-methylmorpholin-4-yl]-8-(trifluoromethyl)-6,7,8,9a-tetrahydro-3H-pyrimido[1,2-a]pyrimidin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1.9 M ammonium sulfate, 100 mM Tris pH 8.5	Resolution 2.90 Å R-free 0.248
4PH4 The crystal structure of Human VPS34 in complex with PIK-III Deposited 2014-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 293–887（595 aa） Fragment：UNP residues 293-887	Not recorded	GOL GLYCEROL × 1 2UG 4'-(cyclopropylmethyl)-N~2~-(pyridin-4-yl)-4,5'-bipyrimidine-2,2'-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；303.15 K；VPS34 protein and PIK-III were mixed and incubated on ice for 1 hr (final PIK-III concentration was 1 mM). Prior to crystallization, the mixture was passed through a 0.2 um filter. The protein:ligand complex was crystallized using the hanging drop vapor diffusion method in Nextal plates: 6 uL of protein solution was mixed with 4 uL of precipitant, which consisted of 20% (w/v) PEG 3350, 100 mM bis-tris propane, and 200 mM Na-K-phosphate. The resulting drop was suspended over a reservoir of 0.3 mL of precipitant and sealed with a screw cap. The crystals grew at 30 degC in approximately 12-24 hr.	Resolution 2.80 Å R-free 0.223
4UWF Discovery of (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: a Novel Potent and Selective Inhibitor of Vps34 for the Treatment of Solid Tumors Deposited 2014-08-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–879（598 aa） Fragment：VPS34 HELICAL AND KINASE DOMAINS, RESIDUES 282-879	Not recorded	EUT (8S)-9-[3,5-bis(fluoranyl)phenyl]-2-morpholin-4-yl-8-(trifluoromethyl)-7,8-dihydro-6H-pyrimido[1,2-a]pyrimidin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；292 K；NA-MALONATE 1.4M, TRIS 100MM PH 8 AT 19C	Resolution 2.99 Å R-free 0.246
4UWG Discovery of (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: a Novel Potent and Selective Inhibitor of Vps34 for the Treatment of Solid Tumors Deposited 2014-08-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–879（598 aa） Fragment：VPS34 HELICAL AND KINASE DOMAINS, RESIDUES 282-879	Not recorded	SO4 SULFATE ION × 3 RBQ (8S)-2-(morpholin-4-yl)-9-[2-(propan-2-yloxy)ethyl]-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；AMMONIUM SULFATE 2M - TRIS 100MM PH 8.5	Resolution 2.70 Å R-free 0.221
4UWH Discovery of (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: a Novel Potent and Selective Inhibitor of Vps34 for the Treatment of Solid Tumors Deposited 2014-08-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–879（598 aa） Fragment：VPS34 HELICAL AND KINASE DOMAINS, RESIDUES 282-879	Not recorded	NA SODIUM ION × 2 JXM (8S)-9-[(2R)-2-hydroxy-2-phenylethyl]-2-(morpholin-4-yl)-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；NA CITRATE 1M PH8.0, pH 7.5	Resolution 1.93 Å R-free 0.208
4UWK Discovery of (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: a Novel Potent and Selective Inhibitor of Vps34 for the Treatment of Solid Tumors Deposited 2014-08-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–879（598 aa） Fragment：VPS34 HELICAL AND KINASE DOMAINS, UNP RESIDUES 282-879	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1 UJB (2S)-1-[(5-chloro-2-thienyl)methyl]-8-[(3R,5R)-3,5-dimethylmorpholin-4-yl]-2-(trifluoromethyl)-3,4-dihydro-2H-pyrimido[1,2-a]pyrimidin-6-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；AMMONIUM SULFATE 1.8M - TRIS 100MM PH 8.5	Resolution 2.83 Å R-free 0.225
4UWL Discovery of (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: a Novel Potent and Selective Inhibitor of Vps34 for the Treatment of Solid Tumors Deposited 2014-08-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–879（598 aa） Fragment：VPS34 HELICAL AND KINASE DOMAINS, RESIDUES 282-879	Not recorded	SO4 SULFATE ION × 2 7A5 (8S)-2-[(3R)-3-methylmorpholin-4-yl]-9-(3-methyl-2-oxobutyl)-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.8M AMMONIUM SULFATE, 100MM TRIS PH 8	Resolution 2.80 Å R-free 0.255
5ANL 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 Deposited 2015-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–879（598 aa） Fragment：VPS34 HELICAL AND KINASE DOMAINS, UNP RESIDUES 282-879	Not recorded	RBQ (8S)-2-(morpholin-4-yl)-9-[2-(propan-2-yloxy)ethyl]-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M TRIS, PH=7.5, 1.8 M AMMONIUM SULFATE	Resolution 2.70 Å R-free 0.267
5ENN The crystal structure of Human VPS34 in complex with a selective and potent inhibitor Deposited 2015-11-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 293–887（595 aa） Fragment：UNP residues 293-887	Not recorded	5QS 1-[[4-(cyclopropylmethyl)-5-[2-(pyridin-4-ylamino)pyrimidin-4-yl]pyrimidin-2-yl]amino]-2-methyl-propan-2-ol × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291.15 K；200nL:200nL well to protein 0.2M Sodium Acetate 0.1M HEPES 7.5 20% PEG 3000	Resolution 2.70 Å R-free 0.201
5ENN The crystal structure of Human VPS34 in complex with a selective and potent inhibitor Deposited 2015-11-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 293–887（595 aa） Fragment：UNP residues 293-887	Not recorded	5QS 1-[[4-(cyclopropylmethyl)-5-[2-(pyridin-4-ylamino)pyrimidin-4-yl]pyrimidin-2-yl]amino]-2-methyl-propan-2-ol × 1 NA SODIUM ION × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291.15 K；200nL:200nL well to protein 0.2M Sodium Acetate 0.1M HEPES 7.5 20% PEG 3000	Resolution 2.70 Å R-free 0.201
6HOG Structure of VPS34 LIR motif bound to GABARAP Deposited 2018-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 244–258（15 aa）	Not recorded	SO4 SULFATE ION × 6 EDO 1,2-ETHANEDIOL × 6 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；50 mM HEPES pH 7.1, 40% PEG 600	Resolution 1.26 Å R-free 0.181
6HOH Structure of VPS34 LIR motif (S249E) bound to GABARAP Deposited 2018-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 244–258（15 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 200 mM magnesium formate	Resolution 2.25 Å R-free 0.250
6HOH Structure of VPS34 LIR motif (S249E) bound to GABARAP Deposited 2018-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 244–258（15 aa） Chain C 244–258（15 aa） Chain D 244–258（15 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 200 mM magnesium formate	Resolution 2.25 Å R-free 0.250
6I3U Optimization of potent and selective ATM inhibitors suitable for a proof-of-concept study in Huntington's disease models Deposited 2018-11-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 268–879（612 aa）	Mutation：F612A, L616N, I634L, M682L, F684W, Q686_S687insG	H2E 2-morpholin-4-yl-6-[7-[(2~{R})-1-morpholin-4-ylpropan-2-yl]oxy-9~{H}-thioxanthen-4-yl]pyran-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.4 M Sodium Malonate pH 7.0, 0.1 M Bis-Tris Propane pH 7.0	Resolution 2.09 Å R-free 0.236
6YKG Structure-based exploration of selectivity for ATM inhibitors in Huntingtons disease Deposited 2020-04-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 268–879（612 aa）	Not recorded	OZ8 4-morpholin-4-yl-6-[(2~{R})-2-(phenylmethyl)pyrrolidin-1-yl]-1~{H}-pyridin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.4 M sodium malonate pH 7.0, 0.1 M BIS-TRIS	Resolution 3.12 Å R-free 0.261
7BL1 human complex II-BATS bound to membrane-attached Rab5a-GTP Deposited 2021-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain BBB 1–887（887 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot force 20, blot time 6 s	Resolution 9.80 Å
7RSJ Structure of the VPS34 kinase domain with compound 14 Deposited 2021-08-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–879（598 aa）	Not recorded	NA SODIUM ION × 3 7IH N-{4-[(7R,8R)-4-oxo-7-(propan-2-yl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazin-2-yl]pyridin-2-yl}cyclopropanecarboxamide × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2M Potassium/Sodium tartrate 0.1M Bis-Tris propane pH7.5, 20% PEG3350 0.7% v/v 1-butanol	Resolution 1.88 Å R-free 0.203
7RSP Structure of the VPS34 kinase domain with compound 14 Deposited 2021-08-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–879（598 aa）	Not recorded	GOL GLYCEROL × 1 7IK (7R,8R)-2-[(3R)-3-methylmorpholin-4-yl]-7-(propan-2-yl)-6,7-dihydropyrazolo[1,5-a]pyrazin-4(5H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2M Potassium/Sodium tartrate, 0.1M Bis-Tris propane pH7.5, 20% PEG3350 0.7% v/v 1-butanol	Resolution 1.67 Å R-free 0.225
7RSP Structure of the VPS34 kinase domain with compound 14 Deposited 2021-08-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 282–879（598 aa）	Not recorded	GOL GLYCEROL × 2 7IK (7R,8R)-2-[(3R)-3-methylmorpholin-4-yl]-7-(propan-2-yl)-6,7-dihydropyrazolo[1,5-a]pyrazin-4(5H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2M Potassium/Sodium tartrate, 0.1M Bis-Tris propane pH7.5, 20% PEG3350 0.7% v/v 1-butanol	Resolution 1.67 Å R-free 0.225
7RSV Structure of the VPS34 kinase domain with compound 5 Deposited 2021-08-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–879（598 aa）	Not recorded	7IQ (5aS,8aR,9S)-2-[(3R)-3-methylmorpholin-4-yl]-5,5a,6,7,8,8a-hexahydro-4H-cyclopenta[e]pyrazolo[1,5-a]pyrazin-4-one × 1 GOL GLYCEROL × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2M Potassium/Sodium tartrate 0.1M Bis-Tris propane pH7.5, 20% PEG3350 0.7% v/v 1-butanol	Resolution 1.78 Å R-free 0.214
7RSV Structure of the VPS34 kinase domain with compound 5 Deposited 2021-08-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 282–879（598 aa）	Not recorded	7IQ (5aS,8aR,9S)-2-[(3R)-3-methylmorpholin-4-yl]-5,5a,6,7,8,8a-hexahydro-4H-cyclopenta[e]pyrazolo[1,5-a]pyrazin-4-one × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2M Potassium/Sodium tartrate 0.1M Bis-Tris propane pH7.5, 20% PEG3350 0.7% v/v 1-butanol	Resolution 1.78 Å R-free 0.214
8RXR Crystal structure of VPS34 in complex with inhibitor SB02024 Deposited 2024-02-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–879（598 aa）	Not recorded	A1H4E 4-[(3R)-3-methylmorpholin-4-yl]-2-[(2R)-2-(trifluoromethyl)piperidin-1-yl]-3H-pyridin-6-one × 1 PEG DI(HYDROXYETHYL)ETHER × 2 IMD IMIDAZOLE × 1 DMS DIMETHYL SULFOXIDE × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；22.5 % PEG3350, 0.2 M ammonium acetate, 0.1 M HEPES pH 8.0	Resolution 2.06 Å R-free 0.225
8RXR Crystal structure of VPS34 in complex with inhibitor SB02024 Deposited 2024-02-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 282–879（598 aa）	Not recorded	A1H4E 4-[(3R)-3-methylmorpholin-4-yl]-2-[(2R)-2-(trifluoromethyl)piperidin-1-yl]-3H-pyridin-6-one × 1 DMS DIMETHYL SULFOXIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；22.5 % PEG3350, 0.2 M ammonium acetate, 0.1 M HEPES pH 8.0	Resolution 2.06 Å R-free 0.225
9C82 Structure of human ULK1C:PI3KC3-C1 supercomplex Deposited 2024-06-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–887（887 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；added 0.05% (w/v) octylglucopyranoside as surfactant	Resolution 6.84 Å
9E4V The structure of human vacuolar protein sorting 34 catalytic domain bound to MES Deposited 2024-10-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 290–871（582 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 1 DMS DIMETHYL SULFOXIDE × 1 PEG DI(HYDROXYETHYL)ETHER × 4 GOL GLYCEROL × 1 CL CHLORIDE ION × 4 K POTASSIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；100mM MES, pH 6.0, 18% PEG3350	Resolution 2.36 Å R-free 0.231
9MHF Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L) Deposited 2024-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–887（887 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å
9MHG Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase domain in the inactive conformation Deposited 2024-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–887（887 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；OG supplemented at time of grid preparation 0.05% cryo-EM vitrification conditions Cryogen ETHANE；100% humidity, 3 s wait time, blot force -15	Resolution 3.20 Å
9MHH PI3KC3-C1 in complex with RAB1A. VPS34 kinase domain active conformation Deposited 2024-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–887（887 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；OG supplemented at time of grid preparation 0.05% cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
9NIN The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-I-86 Deposited 2025-02-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 290–871（582 aa）	Not recorded	A1BYW 2-[(8R)-pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-benzothiazol-6-ol × 1 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 14 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；0.1 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v Polyethylene glycol 10,000	Resolution 2.01 Å R-free 0.212
9ORM The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-I-137 Deposited 2025-05-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 290–871（582 aa）	Not recorded	A1CD6 ethyl 2-[(8S)-pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-benzothiazole-6-carboxylate × 1 GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；0.1 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v Polyethylene glycol 10,000	Resolution 2.06 Å R-free 0.227
9RX5 VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L) Deposited 2025-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–887（887 aa）	Mutation：199-REIE-202 to 199-AAAA-202	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.15 Å
9RX6 VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15 subunit Deposited 2025-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–887（887 aa）	Mutation：199-REIE-202 to 199-ERIR-202	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.52 Å
9RX8 Apo VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) Deposited 2025-07-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–887（887 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.87 Å
9RX9 VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS34 subunit Deposited 2025-07-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–887（887 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.99 Å
9RXA VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS15 subunit Deposited 2025-07-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–887（887 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 4.00 Å
9RXB VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) bound to RAB5A (Q79L) on the VPS34 and VPS15 subunits Deposited 2025-07-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–887（887 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 4.03 Å
9S47 Human complex II-BATS bound to membrane-attached Rab5a-GTP Deposited 2025-07-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–887（887 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 9.88 Å
9ZF4 The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-83 Deposited 2025-12-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 290–871（582 aa）	Not recorded	A1C15 methyl 2-[(8R)-pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-benzothiazole-6-carboxylate × 1 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 5 DMS DIMETHYL SULFOXIDE × 1 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 2 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；0.2 M Sodium Chloride, 25% w/v Polyethylene glycol 3,350	Resolution 2.09 Å R-free 0.224
9ZPC Cryo-EM structure of human PI3KC3-C2 Deposited 2025-12-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–887（887 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.83 Å
9ZPD Cryo-EM structure of human PI3KC3-C2 in complex with Rubicon Middle Region of C terminus Deposited 2025-12-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–887（887 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å

40 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PK3C3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 13–594； UniProt 290–871

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9dkp
Deposition date deposition_date	2024-09-09
最后修订 last_revision	2025-09-17
Structure title title	The structure of human vacuolar protein sorting 34 catalytic domain bound to RD-I-53
Keywords keywords	Phosphatidylinositol 3-phosphate, Lipid regulator, autophagy, membrane trafficking, endocytosis, enzyme, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.56 Å
Radius of gyration Rg (electron density) rg_electron	24.64 Å
Forward intensity I(0) i0	108578000.00
Molecular weight molecular_weight	55346.0 kDa
Excluded volume excluded_volume	53855 Å³
Envelope volume envelope_volume	87766 Å³
Hydration-shell volume shell_volume	29577 Å³
Envelope diameter envelope_diameter	84.8 Å
Shell Rg shell_rg	32.12 Å
Envelope Rg envelope_rg	24.83 Å
Shape Rg shape_rg	24.59 Å
Total Rg total_rg	25.33 Å
Total atoms total_atoms	4201
Residues n_residues	529
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	82.5 Å
Rg (real space) rg_real	25.49 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.0860e+08
I(0) uncertainty (real space) i0_real_error	1.5910e+06
Rg (reciprocal space) rg_reciprocal	25.51 Å
I(0) (reciprocal space) i0_reciprocal	108600000.0000
Solution quality estimate total_estimate	0.8999
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.6 Å
Skewness Skewness skewness	0.244
Kurtosis Kurtosis kurtosis	-0.430
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16200000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Phosphatidylinositol 3-kinase catalytic subunit type 3
Molecular weight formula_weight	68149.9 kDa
EC 编号 ec_number	2.7.1.137
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	4386

MGHHHHHHHHHHAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	(8R)-3-(1,3-benzothiazol-2-yl)pyrazolo[1,5-a]pyrimidine
Molecular weight formula_weight	252.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-ETHOXYETHANOL
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	diethyl ether
Molecular weight formula_weight	74.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	112

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8. Citations (1)

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Unit-cell length a length_a	113.506 Å
Unit-cell length b length_b	113.506 Å
Unit-cell length c length_c	145.235 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	tetragonal

Resolution resolution	2.160 Å
Low-resolution limit resolution_low	53.850 Å
R factor r_factor	0.2082
R_work r_work	0.2068
R_free r_free	0.2353

fit	/app/data/saxs_computation/dk/9dkp/9dkp.fit
pddf	/app/data/pr_computation/dk/9dkp/9dkp.pr.out
profile	/app/data/saxs_computation/dk/9dkp/9dkp.dat