SAXSdb — 3k9m

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

Cathepsin B

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 80–333	Not recorded	Cystatin-A × 1 （P01040）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2M ammonium suphate, 24% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.61 Å R-free 0.250
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 80–333	Not recorded	Cystatin-A × 1 （P01040）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2M ammonium suphate, 24% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.61 Å R-free 0.250

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 3K9M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CSB Crystal structure of cathepsin b inhibited with CA030 at 2.1 angstroms resolution: A basis for the design of specific epoxysuccinyl inhibitors Deposited 1994-12-09	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 80–126（47 aa） Chain B 129–333（205 aa）	Not recorded	EP0 N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-isoleucyl-L-proline × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1CSB Crystal structure of cathepsin b inhibited with CA030 at 2.1 angstroms resolution: A basis for the design of specific epoxysuccinyl inhibitors Deposited 1994-12-09	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 D 80–126（47 aa） Chain E 129–333（205 aa）	Not recorded	EP0 N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-isoleucyl-L-proline × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1GMY Cathepsin B complexed with dipeptidyl nitrile inhibitor Deposited 2001-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 79–339（261 aa） Fragment：PROTEASE DOMAIN, RESIDUES 80-333	Not recorded	AEM 2-AMINOETHANIMIDIC ACID × 1 APD 3-METHYLPHENYLALANINE × 1 DFA DIPHENYLACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.50	Resolution 1.90 Å R-free 0.199
1GMY Cathepsin B complexed with dipeptidyl nitrile inhibitor Deposited 2001-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 79–339（261 aa） Fragment：PROTEASE DOMAIN, RESIDUES 80-333	Not recorded	AEM 2-AMINOETHANIMIDIC ACID × 1 APD 3-METHYLPHENYLALANINE × 1 DFA DIPHENYLACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.50	Resolution 1.90 Å R-free 0.199
1GMY Cathepsin B complexed with dipeptidyl nitrile inhibitor Deposited 2001-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 79–339（261 aa） Fragment：PROTEASE DOMAIN, RESIDUES 80-333	Not recorded	AEM 2-AMINOETHANIMIDIC ACID × 1 APD 3-METHYLPHENYLALANINE × 1 DFA DIPHENYLACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.50	Resolution 1.90 Å R-free 0.199
1HUC THE REFINED 2.15 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF HUMAN LIVER CATHEPSIN B: THE STRUCTURAL BASIS FOR ITS SPECIFICITY Deposited 1993-04-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 80–126（47 aa） Chain B 129–333（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1HUC THE REFINED 2.15 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF HUMAN LIVER CATHEPSIN B: THE STRUCTURAL BASIS FOR ITS SPECIFICITY Deposited 1993-04-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 80–126（47 aa） Chain D 129–333（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1PBH CRYSTAL STRUCTURE OF HUMAN RECOMBINANT PROCATHEPSIN B AT 3.2 ANGSTROM RESOLUTION Deposited 1997-02-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–333（316 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.3；PROTEIN WAS CRYSTALLIZED FROM 30% PEG 6000, 0.2 M AMMONIUM SULFATE, 0.1 M HEPES, PH 7.3	Resolution 3.20 Å R-free 0.252
2IPP Crystal Structure of the tetragonal form of human liver cathepsin B Deposited 2006-10-12	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 80–126（47 aa） Fragment：light chain, residues 80-126 Chain B 129–333（205 aa） Fragment：heavy chain, residues 129-333	Not recorded	PYS 2-PYRIDINETHIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.15 Å
2PBH CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 3.3 ANGSTROM RESOLUTION Deposited 1997-02-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–333（316 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, 700 MM TRIS, PH 7.2	Resolution 3.30 Å R-free 0.269
3AI8 Cathepsin B in complex with the nitroxoline Deposited 2010-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 78–333（256 aa）	Not recorded	HNQ 5-nitroquinolin-8-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3；293 K；0.1M citric acid, 21% PEG6000, pH 3.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.11 Å R-free 0.244
3AI8 Cathepsin B in complex with the nitroxoline Deposited 2010-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–333（256 aa）	Not recorded	HNQ 5-nitroquinolin-8-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3；293 K；0.1M citric acid, 21% PEG6000, pH 3.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.11 Å R-free 0.244
3CBJ Chagasin-Cathepsin B complex Deposited 2008-02-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 74–339（266 aa）	Mutation：C29A, H110A, S115A	PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.2 M ammonium dihydrogen phosphate, 20% PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.210
3CBJ Chagasin-Cathepsin B complex Deposited 2008-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 74–339（266 aa）	Mutation：C29A, H110A, S115A	PO4 PHOSPHATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.2 M ammonium dihydrogen phosphate, 20% PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.210
3CBK chagasin-cathepsin B Deposited 2008-02-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 74–339（266 aa）	Mutation：C29A, H110A, S115A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；0.14M ammonium fluoride, 14% PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.67 Å R-free 0.242
3PBH REFINED CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 2.5 ANGSTROM RESOLUTION Deposited 1997-02-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–333（316 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.72；PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, PH 5.72	Resolution 2.50 Å R-free 0.234
5MBL Cathepsin B in complex with DARPin 81 Deposited 2016-11-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 78–333（256 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；292 K；buffer: 50mM Tris/HCl, 300mM NaCl, 0.05% Tween-20 precipitant: 0.1M MES, 1.8M NH4SO4	Resolution 1.81 Å R-free 0.193
5MBM Cathepsin B in complex with DARPin 8h6 Deposited 2016-11-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 78–333（256 aa） Fragment：UNP residues 78-333	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0,1 M Na-citrate 15% PEG6000	Resolution 2.76 Å R-free 0.281
5MBM Cathepsin B in complex with DARPin 8h6 Deposited 2016-11-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 78–333（256 aa） Fragment：UNP residues 78-333	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0,1 M Na-citrate 15% PEG6000	Resolution 2.76 Å R-free 0.281
6AY2 Structure of CathB with covalently linked Compound 28 Deposited 2017-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 79–333（255 aa）	Not recorded	C1G N~1~-[(2S)-1-amino-5-(carbamoylamino)pentan-2-yl]-N'~1~-[(1R)-1-(thiophen-3-yl)ethyl]cyclobutane-1,1-dicarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；295 K；as published	Resolution 1.60 Å R-free 0.176
6AY2 Structure of CathB with covalently linked Compound 28 Deposited 2017-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 79–333（255 aa）	Not recorded	C1G N~1~-[(2S)-1-amino-5-(carbamoylamino)pentan-2-yl]-N'~1~-[(1R)-1-(thiophen-3-yl)ethyl]cyclobutane-1,1-dicarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；295 K；as published	Resolution 1.60 Å R-free 0.176
8B4T Human cathepsin B in complex with the carbamate inhibitor 7 Deposited 2022-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 79–333（255 aa）	Mutation：S115A	P9F (2S)-2-[[(2S)-2-[(4-chloranylphenoxy)carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1 M Sodium Acetate pH 5.5, 20% PEG 2000 MME	Resolution 1.45 Å R-free 0.208
8B5F Human cathepsin B in complex with the carbamate inhibitor 31 Deposited 2022-09-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 79–333（255 aa）	Mutation：S115A	P9U (2S)-2-[[(2S)-2-[[3-chloranyl-4-[[3-phenyl-2-(phenylmethyl)propanoyl]amino]phenoxy]carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1 M Sodium Acetate pH 5.5, 30% PEG 5000 MME	Resolution 1.70 Å R-free 0.205
8HE9 Crystal structure of CTSB in complex with K777 Deposited 2022-11-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 79–333（255 aa）	Not recorded	0IW Nalpha-[(4-methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-phenylalaninamide × 1 GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；17.1 % v/v Polyethylene glycol 600, 50 mM MES pH 5.6, 8.6 % w/v Polyethylene glycol 4,000	Resolution 1.55 Å R-free 0.202
8HEI Crystal structure of CTSB in complex with E64d Deposited 2022-11-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 77–333（257 aa）	Not recorded	E6D ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000	Resolution 1.55 Å R-free 0.173
8HEN Crystal structure of CTSB in complex with 212-148 Deposited 2022-11-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 77–333（257 aa）	Not recorded	GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 1 L4F 2-[4-[[(2~{S})-1-oxidanylidene-3-phenyl-1-[[(3~{S})-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]amino]propan-2-yl]carbamoyl]piperazin-1-yl]ethyl 4-carbamimidamidobenzoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Magnesium chloride hexahydrate, 0.1 M NaAc pH 5.2, 28% w/v PEG 3350	Resolution 1.95 Å R-free 0.232
9VA8 Crystal Structure of Human Cathepsin B with a L-peptide substrate Deposited 2025-06-03	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 80–333（254 aa）	Mutation：S115A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane	Resolution 1.50 Å R-free 0.209
9XHR Crystal Structure of Human Cathepsin B with a D-peptide substrate Deposited 2025-11-02	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 79–333（255 aa）	Mutation：S115A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M bicine, 20% PEG 10K	Resolution 1.50 Å R-free 0.170

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

View Construct and Data Evidence

UniProt name	CATB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–254； UniProt 80–333 Author chain B； PDBConstruct 1–254； UniProt 80–333

Cystatin-A

Homo sapiens

UniProt P01040

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–98	Not recorded	Cathepsin B × 1 （P07858）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2M ammonium suphate, 24% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.61 Å R-free 0.250
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–98	Not recorded	Cathepsin B × 1 （P07858）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.2M ammonium suphate, 24% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.61 Å R-free 0.250

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 3K9M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CYU SOLUTION NMR STRUCTURE OF RECOMBINANT HUMAN CYSTATIN A UNDER THE CONDITION OF PH 3.8 AND 310K Deposited 1995-08-24	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–98（98 aa）	Mutation：DEL(M1), M65L	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CYV SOLUTION NMR STRUCTURE OF RECOMBINANT HUMAN CYSTATIN A UNDER THE CONDITION OF PH 3.8 AND 310K Deposited 1995-08-24	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–98（98 aa）	Mutation：DEL(M1), M65L	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1DVC SOLUTION NMR STRUCTURE OF HUMAN STEFIN A AT PH 5.5 AND 308K, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-02-26	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–98（98 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；308 K	Resolution not provided
1DVD SOLUTION NMR STRUCTURE OF HUMAN STEFIN A AT PH 5.5 AND 308K, NMR, 17 STRUCTURES Deposited 1996-02-26	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–98（98 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；308 K	Resolution not provided
1GD3 refined solution structure of human cystatin A Deposited 2000-09-08	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–98（98 aa）	Mutation：M65L	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；310 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1.4mM cystatin A U-15N,13C; 10mM Acetate buffer NA; 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 1.4mM cystatin A U-15N; 10mM Acetate buffer NA; 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 1.4mM cystatin A; 10mM Acetate buffer NA; 98% D2O \| 98% D2O	Resolution not provided
1GD4 SOLUTION STRUCTURE OF P25S CYSTATIN A Deposited 2000-09-08	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–98（98 aa）	Mutation：M65L,P25S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；310 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1.4mM P25S cystatin A U-15N,13C; 10mM Acetate buffer ; 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 1.4mM P25S cystatin A U-15N; 10mM Acetate buffer ; 90% H2O 10% D2O \| 95% H2O/5% D2O NMR sample composition 1.4mM P25S cystatin A; 10mM Acetate buffer ; 98% D2O \| 98% D2O	Resolution not provided
1N9J Solution Structure of the 3D domain swapped dimer of Stefin A Deposited 2002-11-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–98（98 aa） Chain B 1–98（98 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；308 K；Pressure ambient NMR sample composition 1.2mM Stefin A U-15N; 50mM phosphate buffer pH 5.5, 100mM KCl, 5mM Azide; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM Stefin A U-15N,13C,2H; 50mM phosphate buffer pH 5.5, 100mM KCl, 5mM Azide; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1NB3 Crystal structure of stefin A in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo-and exopeptidases Deposited 2002-12-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.246
1NB3 Crystal structure of stefin A in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo-and exopeptidases Deposited 2002-12-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.246
1NB3 Crystal structure of stefin A in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo-and exopeptidases Deposited 2002-12-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.246
1NB3 Crystal structure of stefin A in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo-and exopeptidases Deposited 2002-12-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.246
1NB5 Crystal structure of stefin A in complex with cathepsin H Deposited 2002-12-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；298 K；PEG 4000, ammonium sulphate, sodium acetate, cadmium chloride, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.274
1NB5 Crystal structure of stefin A in complex with cathepsin H Deposited 2002-12-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；298 K；PEG 4000, ammonium sulphate, sodium acetate, cadmium chloride, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.274
1NB5 Crystal structure of stefin A in complex with cathepsin H Deposited 2002-12-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；298 K；PEG 4000, ammonium sulphate, sodium acetate, cadmium chloride, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.274
1NB5 Crystal structure of stefin A in complex with cathepsin H Deposited 2002-12-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；298 K；PEG 4000, ammonium sulphate, sodium acetate, cadmium chloride, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.274
3KFQ Unreduced cathepsin V in complex with stefin A Deposited 2009-10-27	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris-HCl, 12% PEG3000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.99 Å R-free 0.219
3KFQ Unreduced cathepsin V in complex with stefin A Deposited 2009-10-27	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris-HCl, 12% PEG3000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.99 Å R-free 0.219
3KSE Unreduced cathepsin L in complex with stefin A Deposited 2009-11-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M Tris-HCl, 16% PEG3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.71 Å R-free 0.204
3KSE Unreduced cathepsin L in complex with stefin A Deposited 2009-11-22	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M Tris-HCl, 16% PEG3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.71 Å R-free 0.204
3KSE Unreduced cathepsin L in complex with stefin A Deposited 2009-11-22	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M Tris-HCl, 16% PEG3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.71 Å R-free 0.204
8GT0 Structure of falcipain and human Stefin A complex Deposited 2022-09-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–98（98 aa）	Not recorded	GOL GLYCEROL × 38 NA SODIUM ION × 10 PEG DI(HYDROXYETHYL)ETHER × 9 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 8 EDO 1,2-ETHANEDIOL × 7 PG4 TETRAETHYLENE GLYCOL × 16 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.05 M cadmium chloride, 0.1 M Na HEPES pH 7.5, 1.0 M sodium acetate and 5 mM MgSO4	Resolution 3.28 Å R-free 0.299
8GT0 Structure of falcipain and human Stefin A complex Deposited 2022-09-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–98（98 aa）	Not recorded	GOL GLYCEROL × 23 NA SODIUM ION × 13 PEG DI(HYDROXYETHYL)ETHER × 11 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 2 EDO 1,2-ETHANEDIOL × 4 PG4 TETRAETHYLENE GLYCOL × 14 SO4 SULFATE ION × 5 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.05 M cadmium chloride, 0.1 M Na HEPES pH 7.5, 1.0 M sodium acetate and 5 mM MgSO4	Resolution 3.28 Å R-free 0.299
8GT7 Structure of falcipain and human Stefin A mutant complex Deposited 2022-09-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–98（98 aa） Chain D 1–98（98 aa）	Mutation：K68R Mutation：K68R	GOL GLYCEROL × 65 NA SODIUM ION × 44 PG4 TETRAETHYLENE GLYCOL × 48 SO4 SULFATE ION × 5 PEG DI(HYDROXYETHYL)ETHER × 54 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 12 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.05 M cadmium chloride, 0.1 M Na HEPES pH 7.5 and 1.5 M sodium acetate	Resolution 3.28 Å R-free 0.300

13 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYTA_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–98； UniProt 1–98 Author chain D； PDBConstruct 1–98； UniProt 1–98

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3k9m
Deposition date deposition_date	2009-10-16
Structure title title	Cathepsin B in complex with stefin A
Keywords keywords	;Disulfide bond, Glycoprotein, Lysosome, Protease, Thiol protease, Zymogen, Thiol protease inhibitor, HYDROLASE-HYDROLASE INHIBITOR complex ;; HYDROLASE/HYDROLASE INHIBITOR
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	30.13 Å
Radius of gyration Rg (electron density) rg_electron	29.54 Å
Forward intensity I(0) i0	102275000.00
Molecular weight molecular_weight	77617.0 kDa
Excluded volume excluded_volume	95895 Å³
Envelope volume envelope_volume	117160 Å³
Hydration-shell volume shell_volume	33674 Å³
Envelope diameter envelope_diameter	105.5 Å
Shell Rg shell_rg	36.01 Å
Envelope Rg envelope_rg	29.50 Å
Shape Rg shape_rg	29.53 Å
Total Rg total_rg	30.14 Å
Total atoms total_atoms	5454
Residues n_residues	704
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	102.1 Å
Rg (real space) rg_real	30.22 Å
Rg uncertainty (real space) rg_real_error	1.09 Å
I(0) (real space) i0_real	1.0230e+08
I(0) uncertainty (real space) i0_real_error	1.6920e+06
Rg (reciprocal space) rg_reciprocal	30.18 Å
I(0) (reciprocal space) i0_reciprocal	102300000.0000
Solution quality estimate total_estimate	0.8763
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.8 Å
Skewness Skewness skewness	0.406
Kurtosis Kurtosis kurtosis	-0.344
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31810000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cathepsin B
Molecular weight formula_weight	27843.0 kDa
EC 编号 ec_number	3.4.22.1
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	5581

LPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDLLTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGSRPPCTGEGDTPKCSKICEPGYSPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGIPRTD

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 polymer

Description description	Cystatin-A
Molecular weight formula_weight	11020.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MIPGGLSEAKPATPEIQEIVDKVKPQLEEKTNETYGKLEAVQYKTQVVAGTNYYIKVRAGDNKYMHLKVFKSLPGQNEDLVLTGYQVDKNKDDELTGF

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3k9mc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

Domain ID domain_id	d3k9md_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

CATH v4.4 (4 domains)

Domain ID domain_id	3k9mA00
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	3k9mB00
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	3k9mC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3k9mD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	62.122 Å
Unit-cell length b length_b	31.078 Å
Unit-cell length c length_c	70.937 Å
Unit-cell angle α angle_alpha	89.95 °
Unit-cell angle β angle_beta	104.45 °
Unit-cell angle γ angle_gamma	89.90 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.610 Å
Low-resolution limit resolution_low	40.520 Å
R factor r_factor	0.2010
R_work r_work	0.1980
R_free r_free	0.2500

fit	/app/data/saxs_computation/k9/3k9m/3k9m.fit
pddf	/app/data/pr_computation/k9/3k9m/3k9m.pr.out
profile	/app/data/saxs_computation/k9/3k9m/3k9m.dat

Cathepsin B in complex with stefin A

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

Cathepsin B

State in the Current Structure

Other States of the Same Protein in the Database

Cystatin-A

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)