1yg6

ClpP

Method: X-RAY DIFFRACTION D_max: 117.9 Å Quality: GOOD

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

ATP-dependent Clp protease proteolytic subunit

Escherichia coli

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 15–207 Chain B； UniProt 15–207 Chain C； UniProt 15–207 Chain D； UniProt 15–207 Chain E； UniProt 15–207 Chain F； UniProt 15–207 Chain G； UniProt 15–207 Chain H； UniProt 15–207 Chain I； UniProt 15–207 Chain J； UniProt 15–207 Chain K； UniProt 15–207 Chain L； UniProt 15–207 Chain M； UniProt 15–207 Chain N； UniProt 15–207	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 14	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；mpd, mes, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.90 Å R-free 0.251

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 1YG6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1TYF THE STRUCTURE OF CLPP AT 2.3 ANGSTROM RESOLUTION SUGGESTS A MODEL FOR ATP-DEPENDENT PROTEOLYSIS Deposited 1997-10-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 15–207（193 aa） Chain B 15–207（193 aa） Chain C 15–207（193 aa） Chain D 15–207（193 aa） Chain E 15–207（193 aa） Chain F 15–207（193 aa） Chain G 15–207（193 aa） Chain H 15–207（193 aa） Chain I 15–207（193 aa） Chain J 15–207（193 aa） Chain K 15–207（193 aa） Chain L 15–207（193 aa） Chain M 15–207（193 aa） Chain N 15–207（193 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.292
2FZS Crystal structure of E. coli ClpP with a Peptide Chloromethyl Ketone Covalently Bound at the Active Site Deposited 2006-02-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 15–207（193 aa） Chain B 15–207（193 aa） Chain C 15–207（193 aa） Chain D 15–207（193 aa） Chain E 15–207（193 aa） Chain F 15–207（193 aa） Chain G 15–207（193 aa） Chain H 15–207（193 aa） Chain I 15–207（193 aa） Chain J 15–207（193 aa） Chain K 15–207（193 aa） Chain L 15–207（193 aa） Chain M 15–207（193 aa） Chain N 15–207（193 aa）	Not recorded	CMQ N~2~-[(BENZYLOXY)CARBONYL]-N-[(1S,2S)-2-HYDROXY-1-(4-HYDROXYBENZYL)PROPYL]-L-LEUCINAMIDE × 14 PGE TRIETHYLENE GLYCOL × 15 GOL GLYCEROL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；0.1M tri-sodium citrate, 0.15M ammonium acetate, 30% PEG 4000 , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.90 Å R-free 0.233
3HLN Crystal structure of ClpP A153C mutant with inter-heptamer disulfide bonds Deposited 2009-05-27	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 15–207（193 aa） Fragment：UNP residues 15-207 Chain B 15–207（193 aa） Fragment：UNP residues 15-207 Chain C 15–207（193 aa） Fragment：UNP residues 15-207 Chain D 15–207（193 aa） Fragment：UNP residues 15-207 Chain E 15–207（193 aa） Fragment：UNP residues 15-207 Chain F 15–207（193 aa） Fragment：UNP residues 15-207 Chain G 15–207（193 aa） Fragment：UNP residues 15-207 Chain H 15–207（193 aa） Fragment：UNP residues 15-207 Chain I 15–207（193 aa） Fragment：UNP residues 15-207 Chain J 15–207（193 aa） Fragment：UNP residues 15-207 Chain K 15–207（193 aa） Fragment：UNP residues 15-207 Chain L 15–207（193 aa） Fragment：UNP residues 15-207 Chain M 15–207（193 aa） Fragment：UNP residues 15-207 Chain N 15–207（193 aa） Fragment：UNP residues 15-207	Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；1 M 1,6-hexanediol, 0.1 M Sodium acetate pH 4.6, 10 mM CoCl2, 100 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.20 Å R-free 0.253
3HLN Crystal structure of ClpP A153C mutant with inter-heptamer disulfide bonds Deposited 2009-05-27	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 1 15–207（193 aa） Fragment：UNP residues 15-207 Chain 2 15–207（193 aa） Fragment：UNP residues 15-207 Chain O 15–207（193 aa） Fragment：UNP residues 15-207 Chain P 15–207（193 aa） Fragment：UNP residues 15-207 Chain Q 15–207（193 aa） Fragment：UNP residues 15-207 Chain R 15–207（193 aa） Fragment：UNP residues 15-207 Chain S 15–207（193 aa） Fragment：UNP residues 15-207 Chain T 15–207（193 aa） Fragment：UNP residues 15-207 Chain U 15–207（193 aa） Fragment：UNP residues 15-207 Chain V 15–207（193 aa） Fragment：UNP residues 15-207 Chain W 15–207（193 aa） Fragment：UNP residues 15-207 Chain X 15–207（193 aa） Fragment：UNP residues 15-207 Chain Y 15–207（193 aa） Fragment：UNP residues 15-207 Chain Z 15–207（193 aa） Fragment：UNP residues 15-207	Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C Mutation：A153C	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；1 M 1,6-hexanediol, 0.1 M Sodium acetate pH 4.6, 10 mM CoCl2, 100 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.20 Å R-free 0.253
3MT6 Structure of ClpP from Escherichia coli in complex with ADEP1 Deposited 2010-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain O 1–207（207 aa） Chain P 1–207（207 aa） Chain Q 1–207（207 aa） Chain R 1–207（207 aa） Chain S 1–207（207 aa） Chain T 1–207（207 aa） Chain U 1–207（207 aa） Chain V 1–207（207 aa） Chain W 1–207（207 aa） Chain X 1–207（207 aa） Chain Y 1–207（207 aa） Chain Z 1–207（207 aa） Chain a 1–207（207 aa） Chain b 1–207（207 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 27	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295.15 K；25-35% (v/v) MPD and 0.1 M sodium acetate at pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 1.90 Å R-free 0.204
3MT6 Structure of ClpP from Escherichia coli in complex with ADEP1 Deposited 2010-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain A 1–207（207 aa） Chain B 1–207（207 aa） Chain C 1–207（207 aa） Chain D 1–207（207 aa） Chain E 1–207（207 aa） Chain F 1–207（207 aa） Chain G 1–207（207 aa） Chain H 1–207（207 aa） Chain I 1–207（207 aa） Chain J 1–207（207 aa） Chain K 1–207（207 aa） Chain L 1–207（207 aa） Chain M 1–207（207 aa） Chain N 1–207（207 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 28	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295.15 K；25-35% (v/v) MPD and 0.1 M sodium acetate at pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 1.90 Å R-free 0.204
6NB1 Crystal structure of Escherichia coli ClpP protease complexed with small molecule activator, ACP1-06 Deposited 2018-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–207（207 aa） Chain B 1–207（207 aa） Chain C 1–207（207 aa） Chain D 1–207（207 aa） Chain E 1–207（207 aa） Chain F 1–207（207 aa） Chain G 1–207（207 aa） Chain H 1–207（207 aa） Chain I 1–207（207 aa） Chain J 1–207（207 aa） Chain K 1–207（207 aa） Chain L 1–207（207 aa） Chain M 1–207（207 aa） Chain N 1–207（207 aa）	Not recorded	KHS N-{2-[(2-chlorophenyl)sulfanyl]ethyl}-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]sulfonyl}propanamide × 14 GOL GLYCEROL × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；294 K；51-63% MPD 0.1 M sodium acetate pH 5.0	Resolution 1.90 Å R-free 0.244
6WR2 ClpP and ClpX IGF loop in ClpX-ClpP complex bound to ssrA tagged GFP Deposited 2020-04-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain H 16–207（192 aa） Chain I 16–207（192 aa） Chain J 16–207（192 aa） Chain K 16–207（192 aa） Chain L 16–207（192 aa） Chain M 16–207（192 aa） Chain N 16–207（192 aa） Chain h 16–207（192 aa） Chain i 16–207（192 aa） Chain j 16–207（192 aa） Chain k 16–207（192 aa） Chain l 16–207（192 aa） Chain m 16–207（192 aa） Chain n 16–207（192 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
6WRF ClpX-ClpP complex bound to GFP-ssrA, recognition complex Deposited 2020-04-29	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 × 14 PDB declaration: tetradecameric	Chain H 16–207（192 aa） Chain I 16–207（192 aa） Chain J 16–207（192 aa） Chain K 16–207（192 aa） Chain L 16–207（192 aa） Chain M 16–207（192 aa） Chain N 16–207（192 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
6WSG ClpX-ClpP complex bound to ssrA-tagged GFP, intermediate complex Deposited 2020-04-30	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 × 14 PDB declaration: tetradecameric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
7MK5 Crystal structure of Escherichia coli ClpP covalently inhibited by clipibicyclene Deposited 2021-04-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 15–207（193 aa） Chain B 15–207（193 aa） Chain C 15–207（193 aa） Chain D 15–207（193 aa） Chain E 15–207（193 aa） Chain F 15–207（193 aa） Chain G 15–207（193 aa） Chain H 15–207（193 aa） Chain I 15–207（193 aa） Chain J 15–207（193 aa） Chain K 15–207（193 aa） Chain L 15–207（193 aa） Chain M 15–207（193 aa） Chain N 15–207（193 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 25 ACT ACETATE ION × 6 ZGV 4-[(1E)-3-{[(2E,4E,6E,8S)-8-hydroxy-4-methyldeca-2,4,6-trienoyl]amino}-3-oxoprop-1-en-1-yl]azete-1(2H)-carboxylic acid × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M sodium acetate, 30% MPD	Resolution 2.95 Å R-free 0.248
7MK5 Crystal structure of Escherichia coli ClpP covalently inhibited by clipibicyclene Deposited 2021-04-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain O 15–207（193 aa） Chain P 15–207（193 aa） Chain Q 15–207（193 aa） Chain R 15–207（193 aa） Chain S 15–207（193 aa） Chain T 15–207（193 aa） Chain U 15–207（193 aa） Chain V 15–207（193 aa） Chain W 15–207（193 aa） Chain X 15–207（193 aa） Chain Y 15–207（193 aa） Chain Z 15–207（193 aa） Chain a 15–207（193 aa） Chain b 15–207（193 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 25 ACT ACETATE ION × 4 ZGV 4-[(1E)-3-{[(2E,4E,6E,8S)-8-hydroxy-4-methyldeca-2,4,6-trienoyl]amino}-3-oxoprop-1-en-1-yl]azete-1(2H)-carboxylic acid × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M sodium acetate, 30% MPD	Resolution 2.95 Å R-free 0.248
8E7V Cryo-EM structure of substrate-free DNClpX.ClpP from singly capped particles Deposited 2022-08-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207 Chain h 16–207（192 aa） Fragment：UNP residues 16-207 Chain i 16–207（192 aa） Fragment：UNP residues 16-207 Chain j 16–207（192 aa） Fragment：UNP residues 16-207 Chain k 16–207（192 aa） Fragment：UNP residues 16-207 Chain l 16–207（192 aa） Fragment：UNP residues 16-207 Chain m 16–207（192 aa） Fragment：UNP residues 16-207 Chain n 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8E8Q Cryo-EM structure of substrate-free DNClpX.ClpP Deposited 2022-08-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207 Chain h 16–207（192 aa） Fragment：UNP residues 16-207 Chain i 16–207（192 aa） Fragment：UNP residues 16-207 Chain j 16–207（192 aa） Fragment：UNP residues 16-207 Chain k 16–207（192 aa） Fragment：UNP residues 16-207 Chain l 16–207（192 aa） Fragment：UNP residues 16-207 Chain m 16–207（192 aa） Fragment：UNP residues 16-207 Chain n 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å
8E91 Cryo-EM structure of substrate-free ClpX.ClpP Deposited 2022-08-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207 Chain h 16–207（192 aa） Fragment：UNP residues 16-207 Chain i 16–207（192 aa） Fragment：UNP residues 16-207 Chain j 16–207（192 aa） Fragment：UNP residues 16-207 Chain k 16–207（192 aa） Fragment：UNP residues 16-207 Chain l 16–207（192 aa） Fragment：UNP residues 16-207 Chain m 16–207（192 aa） Fragment：UNP residues 16-207 Chain n 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.57 Å
8ET3 Cryo-EM structure of a delivery complex containing the SspB adaptor, an ssrA-tagged substrate, and the AAA+ ClpXP protease Deposited 2022-10-16	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 × 16 PDB declaration: hexadecameric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8V9R Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Branched-Degron DHFR-ssrA Substrate Bound with MTX Deposited 2023-12-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain h 16–207（192 aa） Fragment：UNP residues 16-207 Chain i 16–207（192 aa） Fragment：UNP residues 16-207 Chain j 16–207（192 aa） Fragment：UNP residues 16-207 Chain k 16–207（192 aa） Fragment：UNP residues 16-207 Chain l 16–207（192 aa） Fragment：UNP residues 16-207 Chain m 16–207（192 aa） Fragment：UNP residues 16-207 Chain n 16–207（192 aa） Fragment：UNP residues 16-207 Chain p 16–207（192 aa） Fragment：UNP residues 16-207 Chain q 16–207（192 aa） Fragment：UNP residues 16-207 Chain r 16–207（192 aa） Fragment：UNP residues 16-207 Chain s 16–207（192 aa） Fragment：UNP residues 16-207 Chain t 16–207（192 aa） Fragment：UNP residues 16-207 Chain u 16–207（192 aa） Fragment：UNP residues 16-207 Chain v 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MTX METHOTREXATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9C87 Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Linear-Degron DHFR-ssrA Substrate Bound with MTX Deposited 2024-06-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain h 16–207（192 aa） Fragment：UNP residues 16-207 Chain i 16–207（192 aa） Fragment：UNP residues 16-207 Chain j 16–207（192 aa） Fragment：UNP residues 16-207 Chain k 16–207（192 aa） Fragment：UNP residues 16-207 Chain l 16–207（192 aa） Fragment：UNP residues 16-207 Chain m 16–207（192 aa） Fragment：UNP residues 16-207 Chain n 16–207（192 aa） Fragment：UNP residues 16-207 Chain p 16–207（192 aa） Fragment：UNP residues 16-207 Chain q 16–207（192 aa） Fragment：UNP residues 16-207 Chain r 16–207（192 aa） Fragment：UNP residues 16-207 Chain s 16–207（192 aa） Fragment：UNP residues 16-207 Chain t 16–207（192 aa） Fragment：UNP residues 16-207 Chain u 16–207（192 aa） Fragment：UNP residues 16-207 Chain v 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MTX METHOTREXATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9C88 Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Translocating a Portion of a Branched-Degron DHFR Substrate Deposited 2024-06-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain h 16–207（192 aa） Fragment：UNP residues 16-207 Chain i 16–207（192 aa） Fragment：UNP residues 16-207 Chain j 16–207（192 aa） Fragment：UNP residues 16-207 Chain k 16–207（192 aa） Fragment：UNP residues 16-207 Chain l 16–207（192 aa） Fragment：UNP residues 16-207 Chain m 16–207（192 aa） Fragment：UNP residues 16-207 Chain n 16–207（192 aa） Fragment：UNP residues 16-207 Chain p 16–207（192 aa） Fragment：UNP residues 16-207 Chain q 16–207（192 aa） Fragment：UNP residues 16-207 Chain r 16–207（192 aa） Fragment：UNP residues 16-207 Chain s 16–207（192 aa） Fragment：UNP residues 16-207 Chain t 16–207（192 aa） Fragment：UNP residues 16-207 Chain u 16–207（192 aa） Fragment：UNP residues 16-207 Chain v 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9PIO Cryo-EM structure of the ClpXP AAA+ protease bound to lambdaO-tagged Arc in a recognition complex 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 × 21 PDB declaration: 21-meric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207 Chain O 16–207（192 aa） Fragment：UNP residues 16-207 Chain P 16–207（192 aa） Fragment：UNP residues 16-207 Chain Q 16–207（192 aa） Fragment：UNP residues 16-207 Chain R 16–207（192 aa） Fragment：UNP residues 16-207 Chain S 16–207（192 aa） Fragment：UNP residues 16-207 Chain T 16–207（192 aa） Fragment：UNP residues 16-207 Chain U 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.61 Å
9PJD Cryo-EM structure of the ClpXP AAA+ protease bound to an unidentified portion of lambdaO-tagged Arc substrate within a translocation complex Deposited 2025-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 20 PDB declaration: 21-meric	Chain H 16–207（192 aa） Fragment：UNP residues 16-207 Chain I 16–207（192 aa） Fragment：UNP residues 16-207 Chain J 16–207（192 aa） Fragment：UNP residues 16-207 Chain K 16–207（192 aa） Fragment：UNP residues 16-207 Chain L 16–207（192 aa） Fragment：UNP residues 16-207 Chain M 16–207（192 aa） Fragment：UNP residues 16-207 Chain N 16–207（192 aa） Fragment：UNP residues 16-207 Chain O 16–207（192 aa） Fragment：UNP residues 16-207 Chain P 16–207（192 aa） Fragment：UNP residues 16-207 Chain Q 16–207（192 aa） Fragment：UNP residues 16-207 Chain R 16–207（192 aa） Fragment：UNP residues 16-207 Chain S 16–207（192 aa） Fragment：UNP residues 16-207 Chain T 16–207（192 aa） Fragment：UNP residues 16-207 Chain U 16–207（192 aa） Fragment：UNP residues 16-207	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.67 Å

18 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CLPP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–193； UniProt 15–207 Author chain B； PDBConstruct 1–193； UniProt 15–207 Author chain C； PDBConstruct 1–193； UniProt 15–207 Author chain D； PDBConstruct 1–193； UniProt 15–207 Author chain E； PDBConstruct 1–193； UniProt 15–207 Author chain F； PDBConstruct 1–193； UniProt 15–207 Author chain G； PDBConstruct 1–193； UniProt 15–207 Author chain H； PDBConstruct 1–193； UniProt 15–207 Author chain I； PDBConstruct 1–193； UniProt 15–207 Author chain J； PDBConstruct 1–193； UniProt 15–207 Author chain K； PDBConstruct 1–193； UniProt 15–207 Author chain L； PDBConstruct 1–193； UniProt 15–207 Author chain M； PDBConstruct 1–193； UniProt 15–207 Author chain N； PDBConstruct 1–193； UniProt 15–207

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	1yg6
Deposition date deposition_date	2005-01-04
Structure title title	ClpP
Keywords keywords	Endopeptidase Clp, Caseinolytic protease, Protease Ti, Heat shock protein F21.5, 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	44.01 Å
Radius of gyration Rg (electron density) rg_electron	43.01 Å
Forward intensity I(0) i0	1272170000.00
Molecular weight molecular_weight	294040.0 kDa
Excluded volume excluded_volume	368320 Å³
Envelope volume envelope_volume	536910 Å³
Hydration-shell volume shell_volume	100280 Å³
Envelope diameter envelope_diameter	122.2 Å
Shell Rg shell_rg	52.74 Å
Envelope Rg envelope_rg	40.16 Å
Shape Rg shape_rg	43.04 Å
Total Rg total_rg	43.36 Å
Total atoms total_atoms	20587
Residues n_residues	2618
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	117.9 Å
Rg (real space) rg_real	43.55 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.2720e+09
I(0) uncertainty (real space) i0_real_error	2.0730e+07
Rg (reciprocal space) rg_reciprocal	44.01 Å
I(0) (reciprocal space) i0_reciprocal	1273000000.0000
Solution quality estimate total_estimate	0.8459
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	65.5 Å
Skewness Skewness skewness	-0.226
Kurtosis Kurtosis kurtosis	-0.613
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	498800000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.236

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ATP-dependent Clp protease proteolytic subunit
Molecular weight formula_weight	21586.9 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	21540

ALVPMVIEQTSRGERSFDIYSRLLKERVIFLTGQVEDHMANLIVAQMLFLEAENPEKDIYLYINSPGGVITAGMSIYDTMQFIKPDVSTICMGQAASMGAFLLTAGAKGKRFCLPNSRVMIHQPLGGYQGQATDIEIHAREILKVKGRMNELMALHTGQSLEQIERDTERDRFLSAPEAVEYGLVDSILTHRN

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	953

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7. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d1yg6a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6i_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6j_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6k_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6l_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6m_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

Domain ID domain_id	d1yg6n_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.1 — Clp protease, ClpP subunit

CATH v4.4 (14 domains)

Domain ID domain_id	1yg6A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6C00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6D00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6E00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6F00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6G00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6H00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6I00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6J00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6K00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6L00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6M00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1yg6N00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	192.500 Å
Unit-cell length b length_b	103.300 Å
Unit-cell length c length_c	159.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	56

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2280
R_work r_work	0.2210
R_free r_free	0.2510

fit	/app/data/saxs_computation/yg/1yg6/1yg6.fit
pddf	/app/data/pr_computation/yg/1yg6/1yg6.pr.out
profile	/app/data/saxs_computation/yg/1yg6/1yg6.dat