Current Protein Identity：P07858
New Search
Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | 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 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 |
| 3K9M Cathepsin B in complex with stefin A Deposited 2009-10-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
80–333（254 aa）
|
Not recorded | No recorded non-water small molecule | 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 |
| 3K9M Cathepsin B in complex with stefin A Deposited 2009-10-16 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
80–333（254 aa）
|
Not recorded | No recorded non-water small molecule | 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 |
| 3PBH REFINED CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 2.5 ANGSTROM RESOLUTION Deposited 1997-02-13 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 |