8hgk

Crystal structure of human ClpP in complex with ZK53

Method: X-RAY DIFFRACTION D_max: 113.8 Å Quality: GOOD

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

ATP-dependent Clp protease proteolytic subunit, mitochondrial

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 homooligomer Homooligomer Protein × 14 PDB declaration: tetradecameric（14） Consistent with protein copy count	Chain A； UniProt 57–277 Chain B； UniProt 57–277 Chain C； UniProt 57–277 Chain D； UniProt 57–277 Chain E； UniProt 57–277 Chain F； UniProt 57–277 Chain G； UniProt 57–277 Chain H； UniProt 57–277 Chain I； UniProt 57–277 Chain J； UniProt 57–277 Chain K； UniProt 57–277 Chain L； UniProt 57–277 Chain M； UniProt 57–277 Chain N； UniProt 57–277	Not recorded	ZLL 4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide × 14 MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；0.2M Magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3350, pH7.9	Resolution 1.90 Å R-free 0.221

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 8HGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1TG6 Crystallography and mutagenesis point to an essential role for the N-terminus of human mitochondrial ClpP Deposited 2004-05-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–277（277 aa） Chain B 1–277（277 aa） Chain C 1–277（277 aa） Chain D 1–277（277 aa） Chain E 1–277（277 aa） Chain F 1–277（277 aa） Chain G 1–277（277 aa）	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 6 EDO 1,2-ETHANEDIOL × 8 GOL GLYCEROL × 6 FME N-FORMYLMETHIONINE × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；100 mM MES pH 6.5, 10 % (V/V) dioxane, 10% glycerol, 1.5-1.8 M (NH4)2SO4 with 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP	Resolution 2.10 Å R-free 0.262
1TG6 Crystallography and mutagenesis point to an essential role for the N-terminus of human mitochondrial ClpP Deposited 2004-05-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–277（277 aa） Chain B 1–277（277 aa） Chain C 1–277（277 aa） Chain D 1–277（277 aa） Chain E 1–277（277 aa） Chain F 1–277（277 aa） Chain G 1–277（277 aa）	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 12 EDO 1,2-ETHANEDIOL × 16 GOL GLYCEROL × 12 FME N-FORMYLMETHIONINE × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；100 mM MES pH 6.5, 10 % (V/V) dioxane, 10% glycerol, 1.5-1.8 M (NH4)2SO4 with 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP	Resolution 2.10 Å R-free 0.262
6BBA Crystal structure of human mitochondrial ClpP complex with acyldepsipeptide ADEP-28 Deposited 2017-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 58–277（220 aa） Fragment：residues 58-277 Chain B 58–277（220 aa） Fragment：residues 58-277 Chain C 58–277（220 aa） Fragment：residues 58-277 Chain D 58–277（220 aa） Fragment：residues 58-277 Chain E 58–277（220 aa） Fragment：residues 58-277 Chain F 58–277（220 aa） Fragment：residues 58-277 Chain G 58–277（220 aa） Fragment：residues 58-277	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；294 K；0.1 M sodium acetate trihydrate pH 4.6, 4% w/v polyethylene glycol 4,000	Resolution 2.80 Å R-free 0.235
6DL7 Human mitochondrial ClpP in complex with ONC201 (TIC10) Deposited 2018-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa）	Not recorded	ONC 7-benzyl-4-[(2-methylphenyl)methyl]-6,7,8,9-tetrahydroimidazo[1,2-a]pyrido[3,4-e]pyrimidin-5(4H)-one × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；277 K；5%(w/v) PEG 4,000, 100mM KCl, 100mM NaAc (pH5.2)	Resolution 2.00 Å R-free 0.262
6H23 Crystal structure of the hClpP Y118A mutant with an activating small molecule Deposited 2018-07-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 57–277（221 aa） Chain B 57–277（221 aa） Chain C 57–277（221 aa） Chain D 57–277（221 aa） Chain E 57–277（221 aa） Chain F 57–277（221 aa） Chain G 57–277（221 aa） Chain H 57–277（221 aa） Chain I 57–277（221 aa） Chain J 57–277（221 aa） Chain K 57–277（221 aa） Chain L 57–277（221 aa） Chain M 57–277（221 aa） Chain N 57–277（221 aa）	Mutation：Y118A Mutation：Y118A Mutation：Y118A Mutation：Y118A Mutation：Y118A Mutation：Y118A Mutation：Y118A Mutation：Y118A Mutation：Y118A Mutation：Y118A Mutation：Y118A Mutation：Y118A Mutation：Y118A Mutation：Y118A	FJT ~{N}-(1,3-benzodioxol-5-ylmethyl)-5-[(2-chloranyl-4-fluoranyl-phenyl)methyl]-1,3,4-oxadiazole-2-carboxamide × 14 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；magnesium chloride, MES, PEG4000	Resolution 3.09 Å R-free 0.261
7UVM Crystal structure of human ClpP protease in complex with TR-27 Deposited 2022-05-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa）	Not recorded	OX0 (10R)-4-[(4-chlorophenyl)methyl]-7-[(3-ethynylphenyl)methyl]-2,4,6,7,8,9-hexahydroimidazo[1,2-a]pyrido[3,4-e]pyrimidin-5(1H)-one × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6 to 5.2, 5 % PEG 4000	Resolution 2.19 Å R-free 0.237
7UVN Crystal structure of human ClpP protease in complex with TR-57 Deposited 2022-05-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa）	Not recorded	P3O 3-({3-[(4-chlorophenyl)methyl]-1-methyl-2,4-dioxo-1,3,4,5,7,8-hexahydropyrido[4,3-d]pyrimidin-6(2H)-yl}methyl)benzonitrile × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate, pH 4.6 to 5.2, 5 % PEG 4000	Resolution 3.11 Å R-free 0.283
7UVR Crystal structure of human ClpP protease in complex with TR-65 Deposited 2022-05-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa）	Not recorded	PJF 3-{[(10R)-4-[(4-chlorophenyl)methyl]-5-oxo-1,2,4,5,8,9-hexahydroimidazo[1,2-a]pyrido[3,4-e]pyrimidin-7(6H)-yl]methyl}benzonitrile × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate pH 4.6 to 5.2, 5% PEG 4000	Resolution 2.86 Å R-free 0.253
7UVU Crystal structure of human ClpP protease in complex with TR-107 Deposited 2022-05-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa）	Not recorded	OY9 3-({3-[(4-chlorophenyl)methyl]-4-oxo-3,5,7,8-tetrahydropyrido[4,3-d]pyrimidin-6(4H)-yl}methyl)benzonitrile × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate, 5% PEG 4000	Resolution 3.24 Å R-free 0.261
7UW0 Crystal structure of human ClpP protease in complex with TR-133 Deposited 2022-05-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa）	Not recorded	P4I 3-({3-[(4-bromophenyl)methyl]-4-oxo-3,5,7,8-tetrahydropyrido[4,3-d]pyrimidin-6(4H)-yl}methyl)benzonitrile × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 sodium acetate, pH 4.6 to 5.2, 5% PEG 4000	Resolution 2.80 Å R-free 0.309
7VP9 Crystal structure of human ClpP in complex with ZG111 Deposited 2021-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 57–277（221 aa） Chain B 57–277（221 aa） Chain C 57–277（221 aa） Chain D 57–277（221 aa） Chain E 57–277（221 aa） Chain F 57–277（221 aa） Chain G 57–277（221 aa） Chain H 57–277（221 aa） Chain I 57–277（221 aa） Chain J 57–277（221 aa） Chain K 57–277（221 aa） Chain L 57–277（221 aa） Chain M 57–277（221 aa） Chain N 57–277（221 aa）	Not recorded	7SR (6S,9aS)-N-[(4-bromophenyl)methyl]-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide × 14 MG MAGNESIUM ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2M sodium bromide, 20% (w/v) polyethylene glycol 3350	Resolution 2.55 Å R-free 0.232
7WH5 Crystal structure of human ClpP in complex with ZG180 Deposited 2021-12-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 57–277（221 aa） Chain B 57–277（221 aa） Chain C 57–277（221 aa） Chain D 57–277（221 aa） Chain E 57–277（221 aa） Chain F 57–277（221 aa） Chain G 57–277（221 aa） Chain H 57–277（221 aa） Chain I 57–277（221 aa） Chain J 57–277（221 aa） Chain K 57–277（221 aa） Chain L 57–277（221 aa） Chain M 57–277（221 aa） Chain N 57–277（221 aa）	Not recorded	9DF (6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide × 14 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3350	Resolution 2.13 Å R-free 0.249
8I7X Crystal structure of human ClpP in complex with ZG36 Deposited 2023-02-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 57–277（221 aa） Chain B 57–277（221 aa） Chain C 57–277（221 aa） Chain D 57–277（221 aa） Chain E 57–277（221 aa） Chain F 57–277（221 aa） Chain G 57–277（221 aa） Chain H 57–277（221 aa） Chain I 57–277（221 aa） Chain J 57–277（221 aa） Chain K 57–277（221 aa） Chain L 57–277（221 aa） Chain M 57–277（221 aa） Chain N 57–277（221 aa）	Not recorded	OSR (6S,9aS)-N-[(4-bromophenyl)methyl]-6-[(2S)-butan-2-yl]-8-[(4-methoxynaphthalen-1-yl)methyl]-4,7-bis(oxidanylidene)-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M sodium bromide, 20% (w/v) polyethylene glycol 3350	Resolution 1.99 Å R-free 0.260
8W7C Activation of mitochondrial Caseinolytic Protease P (ClpP) induces selective cancer cell lethality Deposited 2023-08-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa）	Not recorded	R89 11-[(3-chlorophenyl)methyl]-7-[[4-(trifluoromethyl)phenyl]methyl]-2,5,7,11-tetrazatricyclo[7.4.0.0^{2,6}]trideca-1(9),3,5-trien-8-one × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；200 mM KCl, 100 mM MES, 12%PEG4000	Resolution 3.00 Å R-free 0.260
8W7E Design, synthesis and biological evaluations of novel small molecular hyper-activators of human caseinolytic peptidase P (hClpP) Deposited 2023-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa） Chain H 58–277（220 aa） Chain I 58–277（220 aa） Chain J 58–277（220 aa） Chain K 58–277（220 aa） Chain L 58–277（220 aa） Chain M 58–277（220 aa） Chain N 58–277（220 aa）	Not recorded	9I3 3-[(3-chlorophenyl)methyl]-6-[(4-chlorophenyl)methyl]-2,4-dihydro-1H-pyrido[2,3-c][2,7]naphthyridin-5-one × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；6% (w/v) PEG 3350, 200 mM KCl, and 100 mM NaAc (pH 6.0)	Resolution 2.80 Å R-free 0.274
8WUZ Development of 2-imino-2,3,5,6,7,8-hexahydropyrido[4,3-d]pyrimidin-4(1H)-one derivatives as human caseinolytic peptidase P (hClpP) activators Deposited 2023-10-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa）	Not recorded	XFU 5-[(3-fluorophenyl)methyl]-9-[[4-(trifluoromethyl)phenyl]methyl]-1,5,9,11-tetrazatricyclo[8.4.0.0^{2,7}]tetradeca-2(7),10-dien-8-one × 14 BR BROMIDE ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298.15 K；0.2 M NaBr, 16% PEG 3350	Resolution 2.90 Å R-free 0.276
8YLB Cocrystal structures of agonists compound 1 with HsClpP Deposited 2024-03-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa） Chain H 58–277（220 aa） Chain I 58–277（220 aa） Chain J 58–277（220 aa） Chain K 58–277（220 aa） Chain L 58–277（220 aa） Chain M 58–277（220 aa） Chain N 58–277（220 aa）	Not recorded	A1LZA 5-[(2-methylphenyl)methyl]-11-(phenylmethyl)-2,5,7,11-tetrazatricyclo[7.4.0.0^{2,6}]trideca-1(9),6-dien-8-one × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；1.6 M Li2SO4 and 0.1 M Tris, pH 8.0	Resolution 2.15 Å R-free 0.260
8YPA Human mitochondrial ClpP in complex with TR89 Deposited 2024-03-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa）	Not recorded	A1LZN (6~{R})-2-[[3,5-bis(fluoranyl)phenyl]methyl]-6-(hydroxymethyl)-5-[[4-(trifluoromethyl)phenyl]methyl]-7,8-dihydro-6~{H}-pyrazolo[1,5-a][1,4]diazepin-4-one × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；289.15 K；0.1 M sodium acetate ph 6.2, 8% PEG 4000	Resolution 2.67 Å R-free 0.258
9DKV Human mitochondrial ClpP in Apo state Deposited 2024-09-10	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: 14-meric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa） Chain H 58–277（220 aa） Chain I 58–277（220 aa） Chain J 58–277（220 aa） Chain K 58–277（220 aa） Chain L 58–277（220 aa） Chain M 58–277（220 aa） Chain N 58–277（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å
9DKW Human mitochondrial ClpP in complex with Bortezomib Deposited 2024-09-10	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: 14-meric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa） Chain H 58–277（220 aa） Chain I 58–277（220 aa） Chain J 58–277（220 aa） Chain K 58–277（220 aa） Chain L 58–277（220 aa） Chain M 58–277（220 aa） Chain N 58–277（220 aa）	Not recorded	BO2 N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.49 Å
9DQK human ClpP - Apo - A192E / E196R Deposited 2024-09-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: 14-meric	Chain A 1–277（277 aa） Chain B 1–277（277 aa） Chain C 1–277（277 aa） Chain D 1–277（277 aa） Chain E 1–277（277 aa） Chain F 1–277（277 aa） Chain G 1–277（277 aa） Chain H 1–277（277 aa） Chain I 1–277（277 aa） Chain J 1–277（277 aa） Chain K 1–277（277 aa） Chain L 1–277（277 aa） Chain M 1–277（277 aa） Chain N 1–277（277 aa）	Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R	CL CHLORIDE ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；200 mM potassium acetate, 35% (v/v) pentaerythritol propoxylate (5/4 PO/OH)	Resolution 2.75 Å R-free 0.250
9DQL human ClpP - Bortezomib - A192E / E196R Deposited 2024-09-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: 14-meric	Chain A 1–277（277 aa） Chain B 1–277（277 aa） Chain C 1–277（277 aa） Chain D 1–277（277 aa） Chain E 1–277（277 aa） Chain F 1–277（277 aa） Chain G 1–277（277 aa） Chain H 1–277（277 aa） Chain I 1–277（277 aa） Chain J 1–277（277 aa） Chain K 1–277（277 aa） Chain L 1–277（277 aa） Chain M 1–277（277 aa） Chain N 1–277（277 aa）	Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R Mutation：A192E, E196R	BO2 N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE × 14 CL CHLORIDE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；200 mM potassium acetate, 35% (v/v) pentaerythritol propoxylate (5/4 PO/OH)	Resolution 3.20 Å R-free 0.237
9DW0 Human ClpX-bound ClpP Deposited 2024-10-08	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain H 58–249（192 aa） Chain I 58–249（192 aa） Chain J 58–249（192 aa） Chain K 58–249（192 aa） Chain L 58–249（192 aa） Chain M 58–249（192 aa） Chain N 58–249（192 aa） Chain O 58–249（192 aa） Chain P 58–249（192 aa） Chain Q 58–249（192 aa） Chain R 58–249（192 aa） Chain S 58–249（192 aa） Chain T 58–249（192 aa） Chain U 58–249（192 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；The sample was prepared using manual blot-and-plunge freezing method in cold room (4 celsius)	Resolution 2.80 Å
9DW1 Human mitochondrial ClpP protease Deposited 2024-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain H 58–277（220 aa） Chain I 58–277（220 aa） Chain J 58–277（220 aa） Chain K 58–277（220 aa） Chain L 58–277（220 aa） Chain M 58–277（220 aa） Chain N 58–277（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；The sample was prepared using manual blot-and-plunge freezing method in cold room (4 celsius)	Resolution 3.40 Å
9DW3 Human mitochondrial ClpP in complex with Bortezomib Deposited 2024-10-08	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 58–277（220 aa） Chain B 58–277（220 aa） Chain C 58–277（220 aa） Chain D 58–277（220 aa） Chain E 58–277（220 aa） Chain F 58–277（220 aa） Chain G 58–277（220 aa） Chain H 58–277（220 aa） Chain I 58–277（220 aa） Chain J 58–277（220 aa） Chain K 58–277（220 aa） Chain L 58–277（220 aa） Chain M 58–277（220 aa） Chain N 58–277（220 aa）	Not recorded	BO2 N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；The sample was prepared using manual blot-and-plunge freezing method in cold room (4 celsius)	Resolution 2.40 Å
9KUF Cryo-EM structure of HsClpP bound to CLPP-2068 Deposited 2024-12-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 59–277（219 aa） Chain B 59–277（219 aa） Chain C 59–277（219 aa） Chain D 59–277（219 aa） Chain E 59–277（219 aa） Chain F 59–277（219 aa） Chain G 59–277（219 aa） Chain H 59–277（219 aa） Chain I 59–277（219 aa） Chain J 59–277（219 aa） Chain K 59–277（219 aa） Chain L 59–277（219 aa） Chain M 59–277（219 aa） Chain N 59–277（219 aa）	Not recorded	A1EG3 3-[[(7~{R})-2-[(4-bromophenyl)methylamino]-7-methyl-4-oxidanylidene-3,5,7,8-tetrahydropyrido[4,3-d]pyrimidin-6-yl]methyl]benzenecarbonitrile × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 8；30 mM Tris-HCl (pH 8.0), 150 mM NaCl and 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.45 Å
9PB1 Human ClpP initial assembly Deposited 2025-06-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain H 58–277（220 aa） Chain I 58–277（220 aa） Chain J 58–277（220 aa） Chain K 58–277（220 aa） Chain L 58–277（220 aa） Chain M 58–277（220 aa） Chain N 58–277（220 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；The sample was prepared using manual blot-and-plunge freezing method in cold room (4 degrees Celsius).	Resolution 3.70 Å
9WAS Human mitochondrial ClpP in complex with LZL25 Deposited 2025-08-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 58–250（193 aa） Chain B 58–250（193 aa） Chain C 58–250（193 aa） Chain D 58–250（193 aa） Chain E 58–250（193 aa） Chain F 58–250（193 aa） Chain G 58–250（193 aa）	Not recorded	A1EVT (3~{R})-7-[(4-fluorophenyl)methyl]-3-(2-methoxyethoxymethyl)-2-[[4-(trifluoromethyl)phenyl]methyl]-3,4-dihydroisoquinolin-1-one × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1M sodium acetate trihydrate pH4.6 8% w/v Polyethylene Glycol 4000	Resolution 3.52 Å R-free 0.247
9YKZ Un-crosslinked hClpP Deposited 2025-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain H 1–277（277 aa） Chain I 1–277（277 aa） Chain J 1–277（277 aa） Chain K 1–277（277 aa） Chain L 1–277（277 aa） Chain M 1–277（277 aa） Chain N 1–277（277 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；The sample was prepared using manual blot-and-plunge freezing method in cold room (4 degrees Celsius)	Resolution 3.50 Å

28 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CLPP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–222； UniProt 57–277 Author chain B； PDBConstruct 2–222； UniProt 57–277 Author chain C； PDBConstruct 2–222； UniProt 57–277 Author chain D； PDBConstruct 2–222； UniProt 57–277 Author chain E； PDBConstruct 2–222； UniProt 57–277 Author chain F； PDBConstruct 2–222； UniProt 57–277 Author chain G； PDBConstruct 2–222； UniProt 57–277 Author chain H； PDBConstruct 2–222； UniProt 57–277 Author chain I； PDBConstruct 2–222； UniProt 57–277 Author chain J； PDBConstruct 2–222； UniProt 57–277 Author chain K； PDBConstruct 2–222； UniProt 57–277 Author chain L； PDBConstruct 2–222； UniProt 57–277 Author chain M； PDBConstruct 2–222； UniProt 57–277 Author chain N； PDBConstruct 2–222； UniProt 57–277

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	8hgk
Deposition date deposition_date	2022-11-14
Structure title title	Crystal structure of human ClpP in complex with ZK53
Keywords keywords	activator, ZK53, human ClpP, HYDROLASE; HYDROLASE
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	42.48 Å
Radius of gyration Rg (electron density) rg_electron	41.37 Å
Forward intensity I(0) i0	1078280000.00
Molecular weight molecular_weight	276630.0 kDa
Excluded volume excluded_volume	348680 Å³
Envelope volume envelope_volume	486450 Å³
Hydration-shell volume shell_volume	93991 Å³
Envelope diameter envelope_diameter	115.5 Å
Shell Rg shell_rg	51.45 Å
Envelope Rg envelope_rg	38.70 Å
Shape Rg shape_rg	41.39 Å
Total Rg total_rg	41.78 Å
Total atoms total_atoms	19302
Residues n_residues	2489
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	113.8 Å
Rg (real space) rg_real	42.04 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	1.0780e+09
I(0) uncertainty (real space) i0_real_error	1.6300e+07
Rg (reciprocal space) rg_reciprocal	42.47 Å
I(0) (reciprocal space) i0_reciprocal	1079000000.0000
Solution quality estimate total_estimate	0.8219
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	64.6 Å
Skewness Skewness skewness	-0.274
Kurtosis Kurtosis kurtosis	-0.621
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	566800000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ATP-dependent Clp protease proteolytic subunit, mitochondrial
Molecular weight formula_weight	24277.0 kDa
EC 编号 ec_number	3.4.21.92
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
Atom count atom_count	19792

SPLIPIVVEQTGRGERAYDIYSRLLRERIVCVMGPIDDSVASLVIAQLLFLQSESNKKPIHMYINSPGGVVTAGLAIYDTMQYILNPICTWCVGQAASMGSLLLAAGTPGMRHSLPNSRIMIHQPSGGARGQATDIAIQAEEIMKLKKQLYNIYAKHTKQSLQVIESAMERDRYMSPMEAQEFGILDKVLVHPPQDGEDEPTLVQKEPVEAAPAAEPVPAST

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

Entity 2 Entity 2 non-polymer

Description description	4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide
Molecular weight formula_weight	424.3 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	478

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8. Citations (1)

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Unit-cell length a length_a	120.310 Å
Unit-cell length b length_b	97.000 Å
Unit-cell length c length_c	123.840 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	28

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.530 Å
R factor r_factor	0.1874
R_work r_work	0.1857
R_free r_free	0.2211

fit	/app/data/saxs_computation/hg/8hgk/8hgk.fit
pddf	/app/data/pr_computation/hg/8hgk/8hgk.pr.out
profile	/app/data/saxs_computation/hg/8hgk/8hgk.dat