5ja7

Human cathepsin K mutant C25S in complex with the allosteric effector NSC94914

Method: X-RAY DIFFRACTION D_max: 94.3 Å Quality: GOOD

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

Cathepsin K

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 107–329	Mutation：C25S	6HM [([1,1'-biphenyl]-2-yl)methyl]propanedioic acid × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2 M ammonium sulfate, 30% (w/v) PEG-8000	Resolution 1.61 Å R-free 0.220
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 107–329	Mutation：C25S	6HM [([1,1'-biphenyl]-2-yl)methyl]propanedioic acid × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2 M ammonium sulfate, 30% (w/v) PEG-8000	Resolution 1.61 Å R-free 0.220

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 5JA7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ATK CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH THE COVALENT INHIBITOR E-64 Deposited 1996-12-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.2；PROTEIN CRYSTALLIZED FROM 10% PEG 8000, 0.1 M NA/K PHOSPHATE AT PH 6.2 CONTAINING 0.2 M NACL AT ROOM TEMPERATURE BY VAPOR DIFFUSION., vapor diffusion	Resolution 2.20 Å R-free 0.310
1AU0 CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT SYMMETRIC DIACYLAMINOMETHYL KETONE INHIBITOR Deposited 1997-09-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	SDK 1,3-BIS[[N-[(PHENYLMETHOXY)CARBONYL]-L-LEUCYL]AMINO]-2-PROPANONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.2；10% ISOPROPANOL,0.1M NAPO4-CITRATE, PH4.2	Resolution 2.60 Å R-free 0.365
1AU2 CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PROPANONE INHIBITOR Deposited 1997-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	POS 1-[[(4-PHENOXYPHENYL)SULFONYL]AMINO]-3-[[N/N-(4-PYRIDINYLCARBONYL)-L-LEUCYL]AMINO]-2-PROPANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；18% PEG 8000, 0.12M LI2SO4, 0.06M SODIUM ACETATE, PH 4.5	Resolution 2.60 Å R-free 0.333
1AU3 CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PYRROLIDINONE INHIBITOR Deposited 1997-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	PCM 1-[N[(PHENYLMETHOXY)CARBONYL]-L-LEUCYL-4-[[N/N-[(PHENYLMETHOXY)CARBONYL]-/NL-LEUCYL]AMINO]-3-PYRROLIDINONE/N × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；28% MPD, 0.1M MES, 0.1M TRIS-HCL, PH 7.0	Resolution 2.50 Å R-free 0.353
1AU4 CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PYRROLIDINONE INHIBITOR Deposited 1997-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	INP 4-[[N-[(PHENYLMETHOXY)CARBONYL]-/NL/N-LEUCYL]AMINO]-1[(2S)-2-[[[4-(PYRIDINYLMETHOXY)CARBONYL]AMINO]-4-METHYLPENT/NYL]-3-PYRROLIDINONE/N × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；30% MPD, 0.1M MES, 0.1M TRIS, PH 7.0	Resolution 2.30 Å R-free 0.370
1AYU CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT SYMMETRIC BISCARBOHYDRAZIDE INHIBITOR Deposited 1997-11-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	INA 1,5-BIS(N-BENZYLOXYCARBONYL-L-LEUCINYL)CARBOHYDRAZIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；30% MPD, 0.1M MES, 0.1M TRIS-HCL, PH7.0	Resolution 2.20 Å R-free 0.318
1AYV CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT THIAZOLHYDRAZIDE INHIBITOR Deposited 1997-11-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	IN6 N-[2-[1-(N-BENZYLOXYCARBONYLAMINO)-3-METHYLBUTYL]THIAZOL-4-YLCARBONYL]-N'-(BENZYLOXYCARBONYL-L-LEUCINYL)HYDRAZIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；30% MPD, 0.1M MES, 0.1M TRIS-HCL, PH7.0	Resolution 2.30 Å R-free 0.312
1AYW CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT BENZYLOXYBENZOYLCARBOHYDRAZIDE INHIBITOR Deposited 1997-11-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	IN3 1-(N-BENZYLOXYCARBONYL-L-LEUCINYL)-5-(3-BENZYLOXY BENZOYL)CARBOHYDRAZIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；22.5% PEG 8000, 0.075M SODIUM ACETATE, 0.15M LITHIUM ACETATE, PH4.5	Resolution 2.40 Å R-free 0.379
1BGO CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PEPTIDOMIMETIC INHIBITOR Deposited 1998-05-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	I10 1-[2-(3-BIPHENYL)-4-METHYLVALERYL)]AMINO-3-(2-PYRIDYLSULFONYL)AMINO-2-PROPANONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 2.30 Å R-free 0.296
1BY8 THE CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN K Deposited 1998-10-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–329（314 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；8-10 % PEG 6000, 0.1M NA CITRATE, PH 5.0	Resolution 2.60 Å R-free 0.344
1MEM Crystal structure of Cathepsin K complexed with a potent vinyl sulfone inhibitor Deposited 1997-01-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	0D6 N-{(1R)-3-phenyl-1-[2-(phenylsulfonyl)ethyl]propyl}-N~2~-(piperazin-1-ylcarbonyl)-L-leucinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；MG FORMATE, UNBUFFERED, pH 6.0	Resolution 1.80 Å
1NL6 Crystal Structure Of The Cysteine Protease Human Cathepsin K In Complex With A Covalent Azepanone Inhibitor Deposited 2003-01-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	750 5-(2-MORPHOLIN-4-YLETHOXY)BENZOFURAN-2-CARBOXYLIC ACID ((S)-3-METHYL-1-{(S)-3-OXO-1-[2-(3-PYRIDIN-2-YLPHENYL)ACETYL]AZEPAN-4-YLCARBAMOYL}BUTYL)AMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；10% PEG 8000, 0.1 M imidazole, 0.2 M calcium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.80 Å R-free 0.298
1NL6 Crystal Structure Of The Cysteine Protease Human Cathepsin K In Complex With A Covalent Azepanone Inhibitor Deposited 2003-01-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 115–329（215 aa）	Not recorded	750 5-(2-MORPHOLIN-4-YLETHOXY)BENZOFURAN-2-CARBOXYLIC ACID ((S)-3-METHYL-1-{(S)-3-OXO-1-[2-(3-PYRIDIN-2-YLPHENYL)ACETYL]AZEPAN-4-YLCARBAMOYL}BUTYL)AMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；10% PEG 8000, 0.1 M imidazole, 0.2 M calcium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.80 Å R-free 0.298
1NLJ CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT AZEPANONE INHIBITOR Deposited 2003-01-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	2CA BENZOFURAN-2-CARBOXYLIC ACID {(S)-3-METHYL-1-[3-OXO-1-(PYRIDIN-2-YLSULFONYL)AZEPAN-4-YLCARBAMOYL]BUTYL}AMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；30% MPD, 0.1 M MES,0.1 M tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.295
1NLJ CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT AZEPANONE INHIBITOR Deposited 2003-01-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 115–329（215 aa）	Not recorded	2CA BENZOFURAN-2-CARBOXYLIC ACID {(S)-3-METHYL-1-[3-OXO-1-(PYRIDIN-2-YLSULFONYL)AZEPAN-4-YLCARBAMOYL]BUTYL}AMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；30% MPD, 0.1 M MES,0.1 M tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.295
1Q6K Cathepsin K complexed with t-butyl(1S)-1-cyclohexyl-2-oxoethylcarbamate Deposited 2003-08-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	SO4 SULFATE ION × 1 TCO TERT-BUTYL(1S)-1-CYCLOHEXYL-2-OXOETHYLCARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；0.2 M ammonium sulfate, 30% PEG8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.10 Å
1SNK Cathepsin K complexed with carbamate derivatized norleucine aldehyde Deposited 2004-03-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 116–329（214 aa）	Not recorded	SO4 SULFATE ION × 3 MYE N2-({[(4-BROMOPHENYL)METHYL]OXY}CARBONYL)-N1-[(1S)-1-FORMYLPENTYL]-L-LEUCINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；295 K；0.2M ammonium sulfate, 30% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.50	Resolution 2.40 Å R-free 0.286
1TU6 Cathepsin K complexed with a ketoamide inhibitor Deposited 2004-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 115–329（215 aa） Fragment：cathepsin K: mature form (residues 115-329) Chain B 115–329（215 aa） Fragment：cathepsin K: mature form (residues 115-329)	Not recorded	SO4 SULFATE ION × 3 FSP [1-(4-FLUOROBENZYL)CYCLOBUTYL]METHYL (1S)-1-[OXO(1H-PYRAZOL-5-YLAMINO)ACETYL]PENTYLCARBAMATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M ammonium sulfate, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.214
1U9V Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABE854 Deposited 2004-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 113–329（217 aa）	Not recorded	IHE 6-(CYCLOHEXYLAMINO)-9-[2-(4-METHYLPIPERAZIN-1-YL)-ETHYL]-9H-PURINE-2-CARBONITRILE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；PEG 4000, Tris, magnesium chloride, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.231
1U9W Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABI491 Deposited 2004-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 113–329（217 aa）	Not recorded	IHI 9-CYCLOPENTYL-6-[2-(3-IMIDAZOL-1-YL-PROPOXY)-PHENYLAMINO]-9H-PURINE-2-CARBONITRILE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, Tris, Lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.226
1U9X Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABJ688 Deposited 2004-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 113–329（217 aa）	Not recorded	IHJ 9-CYCLOPENTYL-6-{2-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPOXY]-PHENYLAMINO}-9H-PURINE-2-CARBONITRILE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；sodium citrate, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.217
1VSN Crystal structure of a potent small molecule inhibitor bound to cathepsin K Deposited 2007-03-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：cathepsin K	Not recorded	NFT N-(2-AMINOETHYL)-N~2~-{(1S)-1-[4'-(AMINOSULFONYL)BIPHENYL-4-YL]-2,2,2-TRIFLUOROETHYL}-L-LEUCINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Mg formate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.209
1YK7 Cathepsin K complexed with a cyanopyrrolidine inhibitor Deposited 2005-01-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：mature form of cathepsin K (sequence database residues 115-329)	Not recorded	NBL N2-[(BENZYLOXY)CARBONYL]-N1-[(3S)-1-CYANOPYRROLIDIN-3-YL]-L-LEUCINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M ammonium sulfate, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.270
1YK8 Cathepsin K complexed with a cyanamide-based inhibitor Deposited 2005-01-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：sequence database residues 115-329	Not recorded	T2M TERT-BUTYL 2-CYANO-2-METHYLHYDRAZINECARBOXYLATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M ammonium sulfate, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.277
1YT7 Cathepsin K complexed with a constrained ketoamide inhibitor Deposited 2005-02-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：sequence database residues 115-329	Not recorded	SO4 SULFATE ION × 2 3FC (1R)-2,2-DIMETHYL-1-({5-[4-(TRIFLUOROMETHYL)PHENYL]-1,3,4-OXADIAZOL-2-YL}METHYL)PROPYL (1S)-1-{OXO[(2-OXO-1,3-OXAZOLIDIN-3-YL)AMINO]ACETYL}PENTYLCARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M AMMONIUM SULFATE, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.251
2ATO Crystal structure of Human Cathepsin K in complex with myocrisin Deposited 2005-08-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	SO4 SULFATE ION × 1 MYQ (S)-(1,2-DICARBOXYETHYLTHIO)GOLD × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；22% MPD, 100 mM acetate buffer, 20 mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.198
2AUX Cathepsin K complexed with a semicarbazone inhibitor Deposited 2005-08-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：mature form of cathepsin K (residues 115-329)	Not recorded	CT1 (1R)-2-METHYL-1-(PHENYLMETHYL)PROPYL[(1S)-1-FORMYLPENTYL]CARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；0.2 M ammonium sulfate, 30% PEG8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.40 Å R-free 0.253
2AUZ Cathepsin K complexed with a semicarbazone inhibitor Deposited 2005-08-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：mature form of cathepsin K (residues 115-329)	Not recorded	SO4 SULFATE ION × 3 CT2 1-(PHENYLMETHYL)CYCLOPENTYL[(1S)-1-FORMYLPENTYL]CARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；0.2M ammonium sulfate, 30% PEG8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP	Resolution 2.30 Å R-free 0.239
2BDL Cathepsin K complexed with a pyrrolidine ketoamide-based inhibitor Deposited 2005-10-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：mature form of cathepsin K (residues 115-329)	Not recorded	4PR (3S)-1-{[(3,5-DIMETHYLISOXAZOL-4-YL)AMINO]CARBONYL}-4,4-DIMETHYLPYRROLIDIN-3-YL{(1S)-1-[1-HYDROXY-2-OXO-2-{[(1R)-1-PHENYLETHYL]AMINO}ETHYL]PENTYL}CARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.2 M ammonium sulfate, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.241
2R6N Crystal structure of a pyrrolopyrimidine inhibitor in complex with human Cathepsin K Deposited 2007-09-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 113–329（217 aa）	Not recorded	CKE 1-{7-cyclohexyl-6-[4-(4-methylpiperazin-1-yl)benzyl]-7H-pyrrolo[2,3-d]pyrimidin-2-yl}methanamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20 % PEG 4000, 10 % Isopropanol, 0.1 M HEPES pH 7.5, vapor diffusion, hanging drop, temperature 298K	Resolution 1.95 Å R-free 0.184
3C9E Crystal structure of the cathepsin K : chondroitin sulfate complex. Deposited 2008-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 115–329（215 aa）	Not recorded	CA CALCIUM ION × 2 E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；Cathepsin K:chondroitin sulfate complex was made at 1:1 ratio. Precipitant contained 30% MPD, 0.1M sodium acetate buffer, 20mM calcium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.80 Å R-free 0.209
3H7D The crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate Deposited 2009-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：UNP residues 115-329	Mutation：K9E, I171E, Q172S, N190M, K191G, L195K	CA CALCIUM ION × 1 E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；30% MPD, 0.1M acetate buffer, 20mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.24 Å R-free 0.238
3H7D The crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate Deposited 2009-04-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 115–329（215 aa） Fragment：UNP residues 115-329	Mutation：K9E, I171E, Q172S, N190M, K191G, L195K	CA CALCIUM ION × 1 E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；30% MPD, 0.1M acetate buffer, 20mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.24 Å R-free 0.238
3H7D The crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate Deposited 2009-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 115–329（215 aa） Fragment：UNP residues 115-329	Mutation：K9E, I171E, Q172S, N190M, K191G, L195K	CA CALCIUM ION × 2 E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；30% MPD, 0.1M acetate buffer, 20mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.24 Å R-free 0.238
3H7D The crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate Deposited 2009-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 115–329（215 aa） Fragment：UNP residues 115-329	Mutation：K9E, I171E, Q172S, N190M, K191G, L195K	CA CALCIUM ION × 2 E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；30% MPD, 0.1M acetate buffer, 20mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.24 Å R-free 0.238
3KW9 X-ray structure of Cathepsin K covalently bound to a triazine ligand Deposited 2009-12-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：UNP residues 115 to 329	Not recorded	ORG 4-(cyclohexylamino)-6-piperazin-1-yl-1,3,5-triazine-2-carbonitrile × 1 TFA trifluoroacetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.9；298 K；30% PEG4000, 0.2M Ammoniumsulphate pH2.9 cryoprotectant: crystallisation solution + 10% PEG4000 , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.259
3KWB Structure of CatK covalently bound to a dioxo-triazine inhibitor Deposited 2009-12-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 115–329（215 aa） Fragment：full length	Mutation：wild type	ORH 3,5-dioxo-4-(3-piperidin-1-ylpropyl)-2-[3-(trifluoromethyl)phenyl]-2,3,4,5-tetrahydro-1,2,4-triazine-6-carbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.4；298 K；30%(W/V) PEG 4000 and 150 mM Ammonium Sulfate pH 3.4 3 microliter of protein at 10 mg/ml and 2 microliter of reservoir solution. , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.02 Å R-free 0.263
3KWB Structure of CatK covalently bound to a dioxo-triazine inhibitor Deposited 2009-12-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain Y 115–329（215 aa） Fragment：full length	Mutation：wild type	ORH 3,5-dioxo-4-(3-piperidin-1-ylpropyl)-2-[3-(trifluoromethyl)phenyl]-2,3,4,5-tetrahydro-1,2,4-triazine-6-carbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.4；298 K；30%(W/V) PEG 4000 and 150 mM Ammonium Sulfate pH 3.4 3 microliter of protein at 10 mg/ml and 2 microliter of reservoir solution. , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.02 Å R-free 0.263
3KWZ Cathepsin K in complex with a non-selective 2-cyano-pyrimidine inhibitor Deposited 2009-12-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：UNP residues 115-329	Not recorded	SO4 SULFATE ION × 6 KWZ 4-(3-piperidin-1-ylpropyl)-6-[3-(trifluoromethyl)phenyl]pyrimidine-2-carbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；26% PEG 4000, 0.1M Tris, 0.2M LiSO4, 15% PEG 400, pH 8.4, VAPOR DIFFUSION, HANGING DROP	Resolution 1.49 Å R-free 0.299
3KX1 Cathepsin K in complex with a selective 2-cyano-pyrimidine inhibitor Deposited 2009-12-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：UNP residues 115-329	Not recorded	KX1 4-cycloheptyl-6-(3-piperidin-1-ylpropyl)pyrimidine-2-carbonitrile × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.9；34% PEG 4000, 0.2M ammonium sulphate pH 2.9, 4% methanol , VAPOR DIFFUSION, HANGING DROP	Resolution 1.51 Å R-free 0.306
3O0U Cathepsin K covalently bound to a cyano-pyrimidine inhibitor with improved selectivity over hERG Deposited 2010-07-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：UNP Residues 115-329	Not recorded	O47 3-{2-[(E)-iminomethyl]-6-propylpyrimidin-4-yl}-N,N-dimethyl-5-(trifluoromethyl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.9；298 K；8% PEG 4K, 0.2 M Ammonium Sulfate pH=3.9, 4% Methanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.217
3O1G Cathepsin K covalently bound to a 2-cyano pyrimidine inhibitor with a benzyl P3 group. Deposited 2010-07-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	SO4 SULFATE ION × 2 O75 N-benzyl-3-(2-cyano-6-propylpyrimidin-4-yl)-N-[2-(dimethylamino)ethyl]-5-(trifluoromethyl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；298 K；Cocrystallization. Protein solution: 20 mM NaAcetate pH 4.0, 0.2 M NaCl. Crystallization condition: 32% PEG 4K, 0.1 M Tris pH 8.4, 0.2 M LiSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å R-free 0.198
3OVZ Cathepsin K in complex with a covalent inhibitor with a ketoamide warhead Deposited 2010-09-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 121–329（209 aa） Fragment：UNP residues 121-329	Not recorded	O96 N-[(1S)-3-amino-1-ethyl-2,3-dioxopropyl]-2-chloro-4-(pyridin-2-ylmethoxy)-3-(trifluoromethyl)benzamide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 298 K；0 mM NaAcetate pH=4.0, 0.3 M NaCl, 20% PEG4000, 0.2 M (NH4)2SO4, pH=2.9, 4% Methanol, Cryoprotectant composition:20% PEG4000, 0.1M (NH4)2SO4 pH=2.9, 4% Methanol, 20% PEG 400, pH 5, cocrystallization, hanging drop, temperature 398K	Resolution 2.02 Å R-free 0.308
4DMX Cathepsin K inhibitor Deposited 2012-02-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：unp residues 115-329	Not recorded	0LB (1R,2R)-N-(1-cyanocyclopropyl)-2-{[4-(4-fluorophenyl)piperazin-1-yl]carbonyl}cyclohexanecarboxamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；PEG, pH 5.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.70 Å R-free 0.206
4DMY Cathepsin K inhibitor Deposited 2012-02-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：unp residues 115-329	Not recorded	0LC (1R,2R)-N-(1-cyanocyclopropyl)-2-[(8-fluoro-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl)carbonyl]cyclohexanecarboxamide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；PEG, pH 5.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.63 Å R-free 0.190
4DMY Cathepsin K inhibitor Deposited 2012-02-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 115–329（215 aa） Fragment：unp residues 115-329	Not recorded	0LC (1R,2R)-N-(1-cyanocyclopropyl)-2-[(8-fluoro-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl)carbonyl]cyclohexanecarboxamide × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；PEG, pH 5.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.63 Å R-free 0.190
4N79 Structure of Cathepsin K-dermatan sulfate complex Deposited 2013-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；VAPOR DIFFUSION	Resolution 2.62 Å R-free 0.260
4N8W cathepsin K - chondroitin sulfate complex Deposited 2013-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；290 K；24% (v/v) 2-methyl-2,4-pentanediol, 100 mM sodium acetate and 100 mM calcium chloride, pH 4.5, VAPOR DIFFUSION, temperature 290K	Resolution 2.02 Å R-free 0.176
4X6H Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. Deposited 2014-12-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：UNP residues 115-329	Not recorded	3XT 4-amino-3-fluoro-N-(1-{[(2Z)-2-iminoethyl]carbamoyl}cyclohexyl)benzamide × 1 I37 4-amino-N-{1-[(cyanomethyl)carbamoyl]cyclohexyl}-3-fluorobenzamide × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；0.1 M Tri-Sodium Citrate, 2.4 M Ammonium Sulfate	Resolution 1.00 Å R-free 0.166
4X6I Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. Deposited 2014-12-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：UNP RESIDUES 115-329	Not recorded	3Y1 2-amino-4-bromo-N-{1-[(cyanomethyl)carbamoyl]cyclohexyl}benzamide × 1 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；Lithium sulfate 0.2M, Sodium acetate 0.1M, Peg 8000 30%	Resolution 1.87 Å R-free 0.237
4X6J Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. Deposited 2014-12-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：UNP RESIDUES 115-329	Not recorded	GOL GLYCEROL × 1 CL CHLORIDE ION × 1 K POTASSIUM ION × 1 PGO S-1,2-PROPANEDIOL × 3 3Y2 2-amino-4-chloro-N-(1-{[(2E)-2-iminoethyl]carbamoyl}cyclohexyl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；Potassium chloride 0.2M, HEPES 0.05M, 5/4 PO/OH 35%	Resolution 1.59 Å R-free 0.238
4YV8 Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal Deposited 2015-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 115–329（215 aa） Fragment：UNP residues 115-329	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294.15 K；24% PEG 8000, 0.2M ammonium sulfate	Resolution 2.00 Å R-free 0.205
4YVA Cathepsin K co-crystallized with actinomycetes extract Deposited 2015-03-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：UNP residues 115-329	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294.15 K；24% PEG 8000, 0.2M Ammonium sulfate	Resolution 1.80 Å R-free 0.210
5J94 Human cathepsin K mutant C25S in complex with the allosteric effector NSC13345 Deposited 2016-04-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–329（223 aa）	Mutation：C25S	1XF 2-{[(carbamoylsulfanyl)acetyl]amino}benzoic acid × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.2 M ammonium sulfate, 30% PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.22 Å R-free 0.234
5JH3 Human cathepsin K mutant C25S Deposited 2016-04-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–329（223 aa）	Not recorded	SO4 SULFATE ION × 2 ACT ACETATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.2 M ammonium sulfate, 30% (w/v) PEG-8000	Resolution 1.75 Å R-free 0.211
5TDI Crystal structure of Cathepsin K with a covalently-linked inhibitor at 1.4 Angstrom resolution. Deposited 2016-09-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Mutation：S49A	7AS 4-fluoro-N-{1-[(Z)-iminomethyl]cyclopropyl}-N~2~-{(1S)-2,2,2-trifluoro-1-[4'-(methylsulfonyl)[1,1'-biphenyl]-4-yl]ethyl }-L-leucinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.05 M cadmium sulfate hydrate, 0.1 M HEPES pH 7.5, 1.0 M sodium acetate trihydrate	Resolution 1.40 Å R-free 0.171
5TUN Crystal structure of uninhibited human Cathepsin K at 1.62 Angstrom resolution Deposited 2016-11-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：UNP residues 115-329	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；294.15 K；20% polyethylene glycol (PEG) 8000, 0.1 M phosphate/citrate pH 4.2 and 0.2 M sodium chloride	Resolution 1.62 Å R-free 0.195
5Z5O Structure of Pycnonodysostosis disease related I249T mutant of human cathepsin K Deposited 2018-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 16–329（314 aa） Chain B 16–88（73 aa）	Mutation：C139S/I249T Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 8 EDO 1,2-ETHANEDIOL × 16 SO4 SULFATE ION × 5 PEG DI(HYDROXYETHYL)ETHER × 7 CL CHLORIDE ION × 1 NA SODIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100mM Na-K Phosphate 6.2, 20 % MPD, 12mM (NH4)2SO4, 10% PEG 3350	Resolution 1.92 Å R-free 0.204
6ASH Crystal structure of human Cathepsin K with a non-active site inhibitor at 1.42 Angstrom resolution Deposited 2017-08-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：UNP residues 115-329	Mutation：S49A	1XF 2-{[(carbamoylsulfanyl)acetyl]amino}benzoic acid × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；295 K；8% polyethylene glycol (PEG) 4000, 0.1 M sodium acetate	Resolution 1.42 Å R-free 0.146
6HGY CRYSTAL STRUCTURE OF CATHEPSIN K WITH N-DESMETHYL THALASSOSPIRAMIDE C Deposited 2018-08-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa） Fragment：CATALYTIC DOMAIN	Not recorded	G4B THALASSOSPIRAMIDE C × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.05M MES pH 6.0, 0.1M Na-Oxalate, 0.1M CaCl2	Resolution 2.20 Å R-free 0.310
6PXF Structure of human Cathepsin K with an ectosteric inhibitor at 1.85 Angstrom resolution Deposited 2019-07-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Mutation：S49A	J0V 1,6,6-trimethyl-10,11-dioxo-6,7,8,9,10,11-hexahydrophenanthro[1,2-b]furan-2-sulfonic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；295 K；0.04 M Potassium phosphate monobasic, 16% w/v PEG8000, 20% v/v glycerol	Resolution 1.85 Å R-free 0.188
6QBS The Alkyne Moiety as a Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K Deposited 2018-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 115–329（215 aa） Chain B 115–329（215 aa）	Not recorded	HVW (2~{S})-4-methyl-~{N}-prop-2-enyl-2-[[(1~{S})-2,2,2-tris(fluoranyl)-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide × 2 CA CALCIUM ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.15 K；0.2 M CaCl2, 20 % PEG-3350	Resolution 1.70 Å R-free 0.210
6QL8 Cathepsin-K in complex with MIV-711 Deposited 2019-01-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 113–329（217 aa）	Not recorded	J5N ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-ethynyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 NO3 NITRATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100mM ADA pH6.0, 500mM ammonium nitrate, 17% PEG 3350	Resolution 1.80 Å R-free 0.181
6QLM Cathepsin-K in complex with MIV-701 Deposited 2019-02-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 114–329（216 aa）	Not recorded	HFH ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{S},6~{a}~{S})-6-fluoranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 300mM NaCl & 20% PEG 5k.mme	Resolution 1.50 Å R-free 0.142
6QLM Cathepsin-K in complex with MIV-701 Deposited 2019-02-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 114–329（216 aa）	Not recorded	HFH ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{S},6~{a}~{S})-6-fluoranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 MHA (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 300mM NaCl & 20% PEG 5k.mme	Resolution 1.50 Å R-free 0.142
6QLW Cathepsin-K in complex with MIV-710 Deposited 2019-02-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 114–329（216 aa）	Not recorded	J5T ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{S})-6-chloranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 CL CHLORIDE ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme	Resolution 2.00 Å R-free 0.225
6QLW Cathepsin-K in complex with MIV-710 Deposited 2019-02-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 114–329（216 aa）	Not recorded	J5T ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{S})-6-chloranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme	Resolution 2.00 Å R-free 0.225
6QLW Cathepsin-K in complex with MIV-710 Deposited 2019-02-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 114–329（216 aa）	Not recorded	J5T ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{S})-6-chloranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 CL CHLORIDE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme	Resolution 2.00 Å R-free 0.225
6QLW Cathepsin-K in complex with MIV-710 Deposited 2019-02-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 114–329（216 aa）	Not recorded	J5T ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{S})-6-chloranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme	Resolution 2.00 Å R-free 0.225
6QLX Cathepsin-K in complex with fluoro-oxa-azabicyclo[3.3.0]octanyl containing inhibitor Deposited 2019-02-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 114–329（216 aa）	Not recorded	HKH ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{S},6~{a}~{S})-6-fluoranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-thiophen-2-yl-benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 400mM sodium chloride and 20% PEG 5k.mme	Resolution 2.10 Å R-free 0.237
6QM0 Cathepsin-K in complex with amino-oxaazabicyclo[3.3.0]octanyl containing inhibitor Deposited 2019-02-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 114–329（216 aa）	Not recorded	MHA (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID × 1 J6B ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-azanyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-3-fluoranyl-4-[2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme	Resolution 1.90 Å R-free 0.174
6QM0 Cathepsin-K in complex with amino-oxaazabicyclo[3.3.0]octanyl containing inhibitor Deposited 2019-02-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 114–329（216 aa）	Not recorded	J6B ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-azanyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-3-fluoranyl-4-[2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme	Resolution 1.90 Å R-free 0.174
7NXL Structure of human cathepsin K in complex with the acrylamide inhibitor Gu3110 Deposited 2021-03-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 114–329（216 aa）	Not recorded	SO4 SULFATE ION × 1 UUK tert-butyl (1-((4-(dibenzylamino)-4-oxobutyl)amino)-4-methyl-1-oxopentan-2-yl)carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；Composition of reservoir solution was 0.1 M MES/imidazole buffer, containing: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.03 M of each NPS (a mix containing sodium nitrate, disodium hydrogen phosphate and ammonium sulfate) additives, pH 6.5. Morpheus C4 condition	Resolution 1.80 Å R-free 0.209
7NXM Structure of human cathepsin K in complex with the selective activity-based probe Gu3416 Deposited 2021-03-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 114–329（216 aa）	Not recorded	SO4 SULFATE ION × 1 UUW N-(4-(dibenzylamino)-4-oxobutyl)-2-(5-(dimethylamino)pentanamido)-4-methylpentanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；Composition of reservoir solution was 0.1 M MES/imidazole buffer, containing: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.03 M of each NPS (a mix containing sodium nitrate, disodium hydrogen phosphate and ammonium sulfate) additives, pH 6.5. Morpheus C4 condition	Resolution 1.72 Å R-free 0.178
7PCK CRYSTAL STRUCTURE OF WILD TYPE HUMAN PROCATHEPSIN K Deposited 1998-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 16–329（314 aa） Chain C 16–329（314 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；100 MM TRIS-HCL, 5% 2-METHYL-2,4-PENTANEDIOL, 12 MM AMMONIUM SULPHATE AND 9% PEG, pH 7.0	Resolution 3.20 Å R-free 0.253
7PCK CRYSTAL STRUCTURE OF WILD TYPE HUMAN PROCATHEPSIN K Deposited 1998-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 16–329（314 aa） Chain D 16–329（314 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；100 MM TRIS-HCL, 5% 2-METHYL-2,4-PENTANEDIOL, 12 MM AMMONIUM SULPHATE AND 9% PEG, pH 7.0	Resolution 3.20 Å R-free 0.253
7QBL Structure of cathepsin K in complex with the 3-cyano-3-aza-beta-amino acid inhibitor Gu2602 Deposited 2021-11-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–329（215 aa）	Not recorded	A0U ~{tert}-butyl ~{N}-[iminomethyl-[2-[methyl-(phenylmethyl)amino]-2-oxidanylidene-ethyl]amino]carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；10% PEG 8000, 20% ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.1 M MES/imidazole pH 6.5	Resolution 2.00 Å R-free 0.286
7QBM Structure of the activation intermediate of cathepsin K in complex with the 3-cyano-3-aza-beta-amino acid inhibitor Gu2602 Deposited 2021-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 114–329（216 aa） Chain P 16–89（74 aa）	Not recorded	A0U ~{tert}-butyl ~{N}-[iminomethyl-[2-[methyl-(phenylmethyl)amino]-2-oxidanylidene-ethyl]amino]carbamate × 1 ACT ACETATE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；10% PEG 8000, 20% ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.1 M MES/imidazole pH 6.5	Resolution 1.88 Å R-free 0.234
7QBN Structure of cathepsin K in complex with the azadipeptide nitrile inhibitor Gu1303 Deposited 2021-11-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 113–329（217 aa）	Not recorded	9ZG (phenylmethyl) ~{N}-[(2~{S})-1-[[aminomethyl(methyl)amino]-methyl-amino]-1-oxidanylidene-3-phenyl-propan-2-yl]carbamate × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulfate, 0.1 M MES/imidazole pH 6.5	Resolution 1.55 Å R-free 0.167
7QBO Structure of the activation intermediate of cathepsin K in complex with the azadipeptide nitrile inhibitor Gu1303 Deposited 2021-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 114–329（216 aa） Chain P 16–89（74 aa）	Not recorded	9ZG (phenylmethyl) ~{N}-[(2~{S})-1-[[aminomethyl(methyl)amino]-methyl-amino]-1-oxidanylidene-3-phenyl-propan-2-yl]carbamate × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；10% PEG 8000, 20% ethylene glycol, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine HCl, 0.02 M DL-serine, 0.1M MES/imidazole pH 6.5	Resolution 1.90 Å R-free 0.212
8C3D Sulfonated Calpeptin is a promising drug candidate against SARS-CoV-2 infections Deposited 2022-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 115–329（215 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30 % PEG-3350, 0.2 M CaCL2	Resolution 2.00 Å R-free 0.227
9G6A Peptide-Small Molecule Hybrids as Novel Selective Irreversible Cathepsin-K Inhibitors in Primary Osteoclasts and Human Lung Cancer Tissue Deposited 2024-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 115–329（215 aa） Chain B 115–329（215 aa）	Not recorded	A1IJC (2~{S})-4-methyl-~{N}-(2-oxidanylidenepropyl)-2-[[(1~{S})-2,2,2-tris(fluoranyl)-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide × 2 PGE TRIETHYLENE GLYCOL × 3 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；293 K；20 % PEG-3350, 0.2 M CaCl2	Resolution 1.99 Å R-free 0.206

69 other PDB entries and 82 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CATK_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–223； UniProt 107–329 Author chain B； PDBConstruct 1–223； UniProt 107–329

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	5ja7
Deposition date deposition_date	2016-04-12
Structure title title	Human cathepsin K mutant C25S in complex with the allosteric effector NSC94914
Keywords keywords	allostery cysteine peptidase proteolysis enzyme regulation collagenase, 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	28.15 Å
Radius of gyration Rg (electron density) rg_electron	27.87 Å
Forward intensity I(0) i0	43796400.00
Molecular weight molecular_weight	49754.0 kDa
Excluded volume excluded_volume	61472 Å³
Envelope volume envelope_volume	76903 Å³
Hydration-shell volume shell_volume	24480 Å³
Envelope diameter envelope_diameter	97.2 Å
Shell Rg shell_rg	33.11 Å
Envelope Rg envelope_rg	27.84 Å
Shape Rg shape_rg	27.85 Å
Total Rg total_rg	28.47 Å
Total atoms total_atoms	3494
Residues n_residues	445
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	94.3 Å
Rg (real space) rg_real	28.46 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	4.3800e+07
I(0) uncertainty (real space) i0_real_error	6.4140e+05
Rg (reciprocal space) rg_reciprocal	28.37 Å
I(0) (reciprocal space) i0_reciprocal	43790000.0000
Solution quality estimate total_estimate	0.8190
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.507
Kurtosis Kurtosis kurtosis	-0.497
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12480000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.716; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.663; Smooth: 0.831

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Cathepsin K
Molecular weight formula_weight	24539.5 kDa
EC 编号 ec_number	3.4.22.38
Mutation mutation	C25S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3939

YIPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSSWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM

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	;[([1,1'-biphenyl]-2-yl)methyl]propanedioic acid ;
Molecular weight formula_weight	270.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	445

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5ja7a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.0 — automated matches

Domain ID domain_id	d5ja7b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5ja7A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	5ja7B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

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8. Citations (1)

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Unit-cell length a length_a	31.620 Å
Unit-cell length b length_b	74.070 Å
Unit-cell length c length_c	90.040 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.610 Å
Low-resolution limit resolution_low	28.060 Å
R factor r_factor	0.1827
R_work r_work	0.1808
R_free r_free	0.2201

fit	/app/data/saxs_computation/ja/5ja7/5ja7.fit
pddf	/app/data/pr_computation/ja/5ja7/5ja7.pr.out
profile	/app/data/saxs_computation/ja/5ja7/5ja7.dat