3hln

Crystal structure of ClpP A153C mutant with inter-heptamer disulfide bonds

Method: X-RAY DIFFRACTION D_max: 182.2 Å Quality: REASONABLE

▼

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	Fragment：UNP residues 15-207 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
2	Protein homooligomer Homooligomer Protein × 14 PDB declaration: tetradecameric（14） Consistent with protein copy count	Chain 1； UniProt 15–207 Chain 2； UniProt 15–207 Chain O； UniProt 15–207 Chain P； UniProt 15–207 Chain Q； UniProt 15–207 Chain R； UniProt 15–207 Chain S； UniProt 15–207 Chain T； UniProt 15–207 Chain U； UniProt 15–207 Chain V； UniProt 15–207 Chain W； UniProt 15–207 Chain X； UniProt 15–207 Chain Y； UniProt 15–207 Chain Z； UniProt 15–207	Fragment：UNP residues 15-207 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

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 3HLN	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 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） 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
1YG6 ClpP Deposited 2005-01-04	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） 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 × 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
2FZS Crystal structure of E. coli ClpP with a Peptide Chloromethyl Ketone Covalently Bound at the Active Site Deposited 2006-02-10	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） 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
3MT6 Structure of ClpP from Escherichia coli in complex with ADEP1 Deposited 2010-04-30	Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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） 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 20 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 1； PDBConstruct 1–193； UniProt 15–207 Author chain 2； PDBConstruct 1–193； UniProt 15–207 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 Author chain O； PDBConstruct 1–193； UniProt 15–207 Author chain P； PDBConstruct 1–193； UniProt 15–207 Author chain Q； PDBConstruct 1–193； UniProt 15–207 Author chain R； PDBConstruct 1–193； UniProt 15–207 Author chain S； PDBConstruct 1–193； UniProt 15–207 Author chain T； PDBConstruct 1–193； UniProt 15–207 Author chain U； PDBConstruct 1–193； UniProt 15–207 Author chain V； PDBConstruct 1–193； UniProt 15–207 Author chain W； PDBConstruct 1–193； UniProt 15–207 Author chain X； PDBConstruct 1–193； UniProt 15–207 Author chain Y； PDBConstruct 1–193； UniProt 15–207 Author chain Z； 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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3hln
Deposition date deposition_date	2009-05-27
Structure title title	Crystal structure of ClpP A153C mutant with inter-heptamer disulfide bonds
Keywords keywords	;disulfide bond, disordered equatorial loops, ATP-binding, Hydrolase, Nucleotide-binding, Protease, Serine protease, Stress response, Zymogen ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	62.20 Å
Radius of gyration Rg (electron density) rg_electron	62.20 Å
Forward intensity I(0) i0	3749620000.00
Molecular weight molecular_weight	513270.0 kDa
Excluded volume excluded_volume	642230 Å³
Envelope volume envelope_volume	1016200 Å³
Hydration-shell volume shell_volume	136300 Å³
Envelope diameter envelope_diameter	198.3 Å
Shell Rg shell_rg	63.54 Å
Envelope Rg envelope_rg	59.90 Å
Shape Rg shape_rg	62.23 Å
Total Rg total_rg	62.14 Å
Total atoms total_atoms	35844
Residues n_residues	4554
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

▼

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

Maximum dimension Dmax dmax	182.2 Å
Rg (real space) rg_real	62.34 Å
Rg uncertainty (real space) rg_real_error	1.36 Å
I(0) (real space) i0_real	3.7490e+09
I(0) uncertainty (real space) i0_real_error	8.0190e+07
Rg (reciprocal space) rg_reciprocal	62.04 Å
I(0) (reciprocal space) i0_reciprocal	3748000000.0000
Solution quality estimate total_estimate	0.5729
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	65.6 Å
Skewness Skewness skewness	0.419
Kurtosis Kurtosis kurtosis	-0.423
Angular range angular_range	— – 0.1250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4539000000.0000
Real-space data points n_real_points	26
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 0.999; Sysdev: 0.004; Positv: 1.000; Valcen: 0.997; Smooth: 0.003

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

Domain ID domain_id	3hln100
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	3hln200
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	3hlnA00
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	3hlnB00
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	3hlnC00
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	3hlnD00
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	3hlnE00
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	3hlnF00
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	3hlnG00
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	3hlnH00
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	3hlnI00
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	3hlnJ00
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	3hlnK00
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	3hlnL00
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	3hlnM00
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	3hlnN00
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	3hlnO00
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	3hlnP00
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	3hlnQ00
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	3hlnR00
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	3hlnS00
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	3hlnT00
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	3hlnU00
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	3hlnV00
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	3hlnW00
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	3hlnX00
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	3hlnY00
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	3hlnZ00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	182.299 Å
Unit-cell length b length_b	182.299 Å
Unit-cell length c length_c	476.859 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	168

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	42.220 Å
R factor r_factor	0.2154
R_work r_work	0.2134
R_free r_free	0.2527

Description description	ATP-dependent Clp protease proteolytic subunit
Molecular weight formula_weight	21618.9 kDa
EC 编号 ec_number	3.4.21.92
Mutation mutation	A153C
Source method src_method	man
Copy count entity_count	28

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2
Atom count atom_count	35844

Crystal structure of ClpP A153C mutant with inter-heptamer disulfide bonds

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

ATP-dependent Clp protease proteolytic subunit

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 28 domains

CATH v4.4 (28 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	13

fit	/app/data/saxs_computation/hl/3hln/3hln.fit
pddf	/app/data/pr_computation/hl/3hln/3hln.pr.out
profile	/app/data/saxs_computation/hl/3hln/3hln.dat