Caspase-3
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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count | Chain A； UniProt 29–175 Chain B； UniProt 176–277 | Fragment：P17 SUBUNIT Fragment：P12 SUBUNIT | acetyl-asp-glu-val-fpr × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；12% PEG-5000, 100 mM Citrate, 10 mM DTT, 3 mM NaN(3), pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K | Resolution 2.50 Å R-free 0.241 |
| 2 | Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain A； UniProt 29–175 Chain B； UniProt 176–277 | Fragment：P17 SUBUNIT Fragment：P12 SUBUNIT | No other associated polymer | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；12% PEG-5000, 100 mM Citrate, 10 mM DTT, 3 mM NaN(3), pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K | Resolution 2.50 Å R-free 0.241 |
| 3 | Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count | Chain A； UniProt 29–175 Chain B； UniProt 176–277 | Fragment：P17 SUBUNIT Fragment：P12 SUBUNIT | acetyl-asp-glu-val-fpr × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；12% PEG-5000, 100 mM Citrate, 10 mM DTT, 3 mM NaN(3), pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K | Resolution 2.50 Å R-free 0.241 |
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 1RHK | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1CP3 CRYSTAL STRUCTURE OF THE COMPLEX OF APOPAIN WITH THE TETRAPEPTIDE INHIBITOR ACE-DVAD-FMC Deposited 1996-12-12 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain B
1–277（277 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；HANGING DROP, RESERVOIR: 5% PEG8000, 0.05 M MAGNESIUM ACETATE, 0.09 M SODIUM CACODYLATE, 0.08 M SODIUM SULFATE, PH 6.4, 4 DEG. CELSIUS, vapor diffusion - hanging drop, temperature 277K
|
Resolution 2.30 Å R-free 0.284 |
| 1GFW THE 2.8 ANGSTROM CRYSTAL STRUCTURE OF CASPASE-3 (APOPAIN OR CPP32)IN COMPLEX WITH AN ISATIN SULFONAMIDE INHIBITOR. Deposited 2000-06-16 | Different construct 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
29–175（147 aa）
Fragment：ACTIVATED MATURE CASPASE-3 (P20) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 29-175)
Chain B
181–277（97 aa）
Fragment：ACTIVATED MATURE CASPASE-3 (P10) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 181-277)
|
Not recorded | MSI 1-METHYL-5-(2-PHENOXYMETHYL-PYRROLIDINE-1-SULFONYL)-1H-INDOLE-2,3-DIONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；4 ul hanging drops were prepared by mixing equal volumes of protein (10 mg/ml in 20 mM HEPES, pH 7.0) and reservoir solution. The drops equilibrated against 500 ul of 15-18% PEG6000, 0.1M sodium citrate, pH 5.9, 20 mM L-cysteine, and 5% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.285 |
| 1GFW THE 2.8 ANGSTROM CRYSTAL STRUCTURE OF CASPASE-3 (APOPAIN OR CPP32)IN COMPLEX WITH AN ISATIN SULFONAMIDE INHIBITOR. Deposited 2000-06-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric |
Chain A
29–175（147 aa）
Fragment：ACTIVATED MATURE CASPASE-3 (P20) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 29-175)
Chain B
181–277（97 aa）
Fragment：ACTIVATED MATURE CASPASE-3 (P10) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 181-277)
|
Not recorded | MSI 1-METHYL-5-(2-PHENOXYMETHYL-PYRROLIDINE-1-SULFONYL)-1H-INDOLE-2,3-DIONE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；4 ul hanging drops were prepared by mixing equal volumes of protein (10 mg/ml in 20 mM HEPES, pH 7.0) and reservoir solution. The drops equilibrated against 500 ul of 15-18% PEG6000, 0.1M sodium citrate, pH 5.9, 20 mM L-cysteine, and 5% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.285 |
| 1GFW THE 2.8 ANGSTROM CRYSTAL STRUCTURE OF CASPASE-3 (APOPAIN OR CPP32)IN COMPLEX WITH AN ISATIN SULFONAMIDE INHIBITOR. Deposited 2000-06-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric |
Chain A
29–175（147 aa）
Fragment：ACTIVATED MATURE CASPASE-3 (P20) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 29-175)
Chain B
181–277（97 aa）
Fragment：ACTIVATED MATURE CASPASE-3 (P10) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 181-277)
|
Not recorded | MSI 1-METHYL-5-(2-PHENOXYMETHYL-PYRROLIDINE-1-SULFONYL)-1H-INDOLE-2,3-DIONE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；4 ul hanging drops were prepared by mixing equal volumes of protein (10 mg/ml in 20 mM HEPES, pH 7.0) and reservoir solution. The drops equilibrated against 500 ul of 15-18% PEG6000, 0.1M sodium citrate, pH 5.9, 20 mM L-cysteine, and 5% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.285 |
| 1GFW THE 2.8 ANGSTROM CRYSTAL STRUCTURE OF CASPASE-3 (APOPAIN OR CPP32)IN COMPLEX WITH AN ISATIN SULFONAMIDE INHIBITOR. Deposited 2000-06-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–175（147 aa）
Fragment：ACTIVATED MATURE CASPASE-3 (P20) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 29-175)
Chain B
181–277（97 aa）
Fragment：ACTIVATED MATURE CASPASE-3 (P10) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 181-277)
|
Not recorded | MSI 1-METHYL-5-(2-PHENOXYMETHYL-PYRROLIDINE-1-SULFONYL)-1H-INDOLE-2,3-DIONE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；4 ul hanging drops were prepared by mixing equal volumes of protein (10 mg/ml in 20 mM HEPES, pH 7.0) and reservoir solution. The drops equilibrated against 500 ul of 15-18% PEG6000, 0.1M sodium citrate, pH 5.9, 20 mM L-cysteine, and 5% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.285 |
| 1GFW THE 2.8 ANGSTROM CRYSTAL STRUCTURE OF CASPASE-3 (APOPAIN OR CPP32)IN COMPLEX WITH AN ISATIN SULFONAMIDE INHIBITOR. Deposited 2000-06-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–175（147 aa）
Fragment：ACTIVATED MATURE CASPASE-3 (P20) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 29-175)
Chain B
181–277（97 aa）
Fragment：ACTIVATED MATURE CASPASE-3 (P10) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 181-277)
|
Not recorded | MSI 1-METHYL-5-(2-PHENOXYMETHYL-PYRROLIDINE-1-SULFONYL)-1H-INDOLE-2,3-DIONE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；4 ul hanging drops were prepared by mixing equal volumes of protein (10 mg/ml in 20 mM HEPES, pH 7.0) and reservoir solution. The drops equilibrated against 500 ul of 15-18% PEG6000, 0.1M sodium citrate, pH 5.9, 20 mM L-cysteine, and 5% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.285 |
| 1I3O CRYSTAL STRUCTURE OF THE COMPLEX OF XIAP-BIR2 AND CASPASE 3 Deposited 2001-02-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–175（175 aa）
Fragment：APOPAIN P17 SUBUNIT
Chain B
176–277（102 aa）
Fragment：APOPAIN P12 SUBUNIT
Chain C
1–175（175 aa）
Fragment：APOPAIN P17 SUBUNIT
Chain D
176–277（102 aa）
Fragment：APOPAIN P12 SUBUNIT
|
Mutation：C285A Mutation：C285A | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.2；295 K；sodium formate, sodium acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.70 Å R-free 0.278 |
| 1NME Structure of Casp-3 with tethered salicylate Deposited 2003-01-09 | Different construct 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
29–174（146 aa）
Fragment：large subunit
Chain B
186–277（92 aa）
Fragment：small subunit
|
Not recorded | 158 3-(2-MERCAPTO-ACETYLAMINO)-4-OXO-PENTANOIC ACID × 1 159 2-HYDROXY-5-(2-MERCAPTO-ETHYLSULFAMOYL)-BENZOIC ACID × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.60 Å R-free 0.205 |
| 1NME Structure of Casp-3 with tethered salicylate Deposited 2003-01-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric |
Chain A
29–174（146 aa）
Fragment：large subunit
Chain B
186–277（92 aa）
Fragment：small subunit
|
Not recorded | 158 3-(2-MERCAPTO-ACETYLAMINO)-4-OXO-PENTANOIC ACID × 4 159 2-HYDROXY-5-(2-MERCAPTO-ETHYLSULFAMOYL)-BENZOIC ACID × 4 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.60 Å R-free 0.205 |
| 1NME Structure of Casp-3 with tethered salicylate Deposited 2003-01-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric |
Chain A
29–174（146 aa）
Fragment：large subunit
Chain B
186–277（92 aa）
Fragment：small subunit
|
Not recorded | 158 3-(2-MERCAPTO-ACETYLAMINO)-4-OXO-PENTANOIC ACID × 4 159 2-HYDROXY-5-(2-MERCAPTO-ETHYLSULFAMOYL)-BENZOIC ACID × 4 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.60 Å R-free 0.205 |
| 1NME Structure of Casp-3 with tethered salicylate Deposited 2003-01-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–174（146 aa）
Fragment：large subunit
Chain B
186–277（92 aa）
Fragment：small subunit
|
Not recorded | 158 3-(2-MERCAPTO-ACETYLAMINO)-4-OXO-PENTANOIC ACID × 2 159 2-HYDROXY-5-(2-MERCAPTO-ETHYLSULFAMOYL)-BENZOIC ACID × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.60 Å R-free 0.205 |
| 1NME Structure of Casp-3 with tethered salicylate Deposited 2003-01-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–174（146 aa）
Fragment：large subunit
Chain B
186–277（92 aa）
Fragment：small subunit
|
Not recorded | 158 3-(2-MERCAPTO-ACETYLAMINO)-4-OXO-PENTANOIC ACID × 2 159 2-HYDROXY-5-(2-MERCAPTO-ETHYLSULFAMOYL)-BENZOIC ACID × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.60 Å R-free 0.205 |
| 1NMQ Extendend Tethering: In Situ Assembly of Inhibitors Deposited 2003-01-10 | Different construct 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
29–277（249 aa）
Fragment：large subunit
Chain B
29–277（249 aa）
Fragment：large subunit
|
Not recorded | 160 3-(3-{2-[(5-METHANESULFONYL-THIOPHENE-2-CARBONYL)-AMINO]-ETHYLDISULFANYLMETHYL}- BENZENESULFONYLAMINO)-4-OXO-PENTANOIC ACID × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.40 Å R-free 0.299 |
| 1NMS Caspase-3 tethered to irreversible inhibitor Deposited 2003-01-10 | Different construct 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
29–277（249 aa）
Fragment：large subunit
Chain B
29–277（249 aa）
Fragment：large subunit
|
Not recorded | 161 5-[4-(1-CARBOXYMETHYL-2-OXO-PROPYLCARBAMOYL)-BENZYLSULFAMOYL]-2-HYDROXY-BENZOIC ACID × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.70 Å R-free 0.183 |
| 1NMS Caspase-3 tethered to irreversible inhibitor Deposited 2003-01-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–277（249 aa）
Fragment：large subunit
Chain B
29–277（249 aa）
Fragment：large subunit
|
Not recorded | 161 5-[4-(1-CARBOXYMETHYL-2-OXO-PROPYLCARBAMOYL)-BENZYLSULFAMOYL]-2-HYDROXY-BENZOIC ACID × 4 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.70 Å R-free 0.183 |
| 1PAU Crystal structure of the complex of apopain with the tetrapeptide aldehyde inhibitor AC-DEVD-CHO Deposited 1996-06-06 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；HANGING DROP VAPOR DIFFUSION. 1.5 MICROLITER DROPS OF PROTEIN:INHIBITOR SOLUTION (8.7 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.5, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (7% PEG-6000 (W/W), 0.10 MOLAR SODIUM CITRATE PH 5.0, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) AND INCUBATED AT ROOM TEMPERATURE, vapor diffusion - hanging drop
|
Resolution 2.50 Å R-free 0.275 |
| 1PAU Crystal structure of the complex of apopain with the tetrapeptide aldehyde inhibitor AC-DEVD-CHO Deposited 1996-06-06 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；HANGING DROP VAPOR DIFFUSION. 1.5 MICROLITER DROPS OF PROTEIN:INHIBITOR SOLUTION (8.7 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.5, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (7% PEG-6000 (W/W), 0.10 MOLAR SODIUM CITRATE PH 5.0, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) AND INCUBATED AT ROOM TEMPERATURE, vapor diffusion - hanging drop
|
Resolution 2.50 Å R-free 0.275 |
| 1PAU Crystal structure of the complex of apopain with the tetrapeptide aldehyde inhibitor AC-DEVD-CHO Deposited 1996-06-06 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；HANGING DROP VAPOR DIFFUSION. 1.5 MICROLITER DROPS OF PROTEIN:INHIBITOR SOLUTION (8.7 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.5, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (7% PEG-6000 (W/W), 0.10 MOLAR SODIUM CITRATE PH 5.0, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) AND INCUBATED AT ROOM TEMPERATURE, vapor diffusion - hanging drop
|
Resolution 2.50 Å R-free 0.275 |
| 1QX3 Conformational restrictions in the active site of unliganded human caspase-3 Deposited 2003-09-04 | 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
29–277（249 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；4-6% PEG 8000, 5-7% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 1.90 Å R-free 0.278 |
| 1RE1 CRYSTAL STRUCTURE OF CASPASE-3 WITH A NICOTINIC ACID ALDEHYDE INHIBITOR Deposited 2003-11-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–175（147 aa）
Fragment：P17 subunit
Chain B
176–277（102 aa）
Fragment：P12 subunit
|
Not recorded | NA3 (3S)-3-{[(5-BROMOPYRIDIN-3-YL)CARBONYL]AMINO}-4-OXOBUTANOIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；12% PEG 5000, 100mM Citrate, 10mM DTT, 3mM NaN(3), pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.50 Å R-free 0.261 |
| 1RHJ CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A PRYAZINONE INHIBITOR Deposited 2003-11-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–175（147 aa）
Fragment：P17 subunit
Chain B
176–277（102 aa）
Fragment：P12 subunit
Chain C
29–175（147 aa）
Fragment：P17 subunit
Chain D
176–277（102 aa）
Fragment：P12 subunit
|
Not recorded | PZN 3-(2-{5-TERT-BUTYL-3-[(4-METHYL-FURAZAN-3-YLMETHYL)-AMINO]-2-OXO-2H-PYRAZIN-1-YL}-BUTYRYLAMINO)-5-(HEXYL-METHYL-AMINO)-4-OXO-PENTANOIC ACID ANION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.8；293 K；16% PEG-6000, 100 mM citrate, 20 mM L-cysteine, 5 mM glycerol, 3 mM NaN(3), pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.252 |
| 1RHM CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A NICOTINIC ACID ALDEHYDE INHIBITOR Deposited 2003-11-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–175（147 aa）
Fragment：P17 SUBUNIT
Chain B
176–277（102 aa）
Fragment：P12 SUBUNIT
Chain C
29–175（147 aa）
Fragment：P17 SUBUNIT
Chain D
176–277（102 aa）
Fragment：P12 SUBUNIT
|
Not recorded | NA4 4-[5-(2-CARBOXY-1-FORMYL-ETHYLCARBAMOYL)-PYRIDIN-3-YL]-BENZOIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；9% PEG-6000, 100 mM citrate, 10 mM DTT, 3 mM NaN(3), pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.50 Å R-free 0.249 |
| 1RHM CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A NICOTINIC ACID ALDEHYDE INHIBITOR Deposited 2003-11-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric |
Chain A
29–175（147 aa）
Fragment：P17 SUBUNIT
Chain B
176–277（102 aa）
Fragment：P12 SUBUNIT
Chain C
29–175（147 aa）
Fragment：P17 SUBUNIT
Chain D
176–277（102 aa）
Fragment：P12 SUBUNIT
|
Not recorded | NA4 4-[5-(2-CARBOXY-1-FORMYL-ETHYLCARBAMOYL)-PYRIDIN-3-YL]-BENZOIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.7；293 K；9% PEG-6000, 100 mM citrate, 10 mM DTT, 3 mM NaN(3), pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.50 Å R-free 0.249 |
| 1RHQ CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A BROMOMETHOXYPHENYL INHIBITOR Deposited 2003-11-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–175（147 aa）
Fragment：P17 SUBUNIT
Chain B
176–277（102 aa）
Fragment：P12 SUBUNIT
Chain D
29–175（147 aa）
Fragment：P17 SUBUNIT
Chain E
176–277（102 aa）
Fragment：P12 SUBUNIT
|
Not recorded | 0ZZ 5-S-benzyl-3-({N-[(5-bromo-2-methoxyphenyl)acetyl]-L-valyl}amino)-2,3-dideoxy-5-thio-D-erythro-pentonic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.93；293 K；7.8% PEG-6000, 100 mM citrate, 120 mM ZnCl(2), 10 mM DTT, 3 mM NaN(3), pH 4.93, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.00 Å R-free 0.354 |
| 1RHR CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A CINNAMIC ACID METHYL ESTER INHIBITOR Deposited 2003-11-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–175（147 aa）
Fragment：P17 subunit
Chain B
176–277（102 aa）
Fragment：P12 subunit
|
Not recorded | CNE (3S)-5-[(2-CHLORO-6-FLUOROBENZYL)SULFANYL]-3-{[N-({2-ETHOXY-5-[(1E)-3-METHOXY-3-OXOPROP-1-ENYL]PHENYL}ACETYL)-D-VALYL]AMINO}-4-OXOPENTANOIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.85；293 K；4% PEG-6000, 100 mM MES, 10 mM DTT, 3 mM NaN(3), pH 5.85, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.00 Å R-free 0.329 |
| 1RHU CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A 5,6,7 TRICYCLIC PEPTIDOMIMETIC INHIBITOR Deposited 2003-11-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–175（147 aa）
Fragment：P17 SUBUNIT
Chain B
176–277（102 aa）
Fragment：P12 SUBUNIT
|
Not recorded | 3CY (3S)-3-[({(2S)-5-[(N-ACETYL-L-ALPHA-ASPARTYL)AMINO]-4-OXO-1,2,4,5,6,7-HEXAHYDROAZEPINO[3,2,1-HI]INDOL-2-YL}CARBONYL)AMINO]-5-(BENZYLSULFANYL)-4-OXOPENTANOIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.5% PEG-6000, 100 mM citrate, 3 mM NaN(3), pH 3.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.51 Å R-free 0.212 |
| 2C1E Crystal structures of caspase-3 in complex with aza-peptide Michael acceptor inhibitors. Deposited 2005-09-14 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Fragment：ALPHA SUBUNIT, RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：BETA SUBUNIT, RESIDUES 176-277
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.75；PEG6000, 100 MM SODIUM CITRATE PH 4.75
|
Resolution 1.77 Å R-free 0.188 |
| 2C2K Crystal structures of caspase-3 in complex with aza-peptide Michael acceptor inhibitors. Deposited 2005-09-29 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Fragment：ALPHA SUBUNIT, RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：BETA SUBUNIT, RESIDUES 176-277
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.75；PEG6000, 100 MM SODIUM CITRATE PH 4.75
|
Resolution 1.87 Å R-free 0.220 |
| 2C2M Crystal structures of caspase-3 in complex with aza-peptide Michael acceptor inhibitors. Deposited 2005-09-29 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Fragment：ALPHA SUBUNIT, RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：BETA SUBUNIT, RESIDUES 176-277
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.75；PEG6000, 100 MM SODIUM CITRATE PH 4.75
|
Resolution 1.94 Å R-free 0.208 |
| 2C2O Crystal structures of caspase-3 in complex with aza-peptide Michael acceptor inhibitors. Deposited 2005-09-29 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Fragment：ALPHA SUBUNIT, RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：BETA SUBUNIT, RESIDUES 176-277
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.75；PEG6000, 100 MM SODIUM CITRATE PH 4.75
|
Resolution 2.45 Å R-free 0.215 |
| 2CDR Crystal structures of caspase-3 in complex with aza-peptide epoxide inhibitors. Deposited 2006-01-27 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
29–175（147 aa）
Fragment：ALPHA SUBUNIT RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：BETA SUBUNIT RESIDUES 176-277
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.75；PEG6000, 100 MM SODIUM CITRATE PH 4.75
|
Resolution 1.70 Å R-free 0.204 |
| 2CJX Extended substrate recognition in caspase-3 revealed by high resolution X-ray structure analysis Deposited 2006-04-09 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Fragment：ALPHA SUBUNIT, RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：BETA SUBUNIT, RESIDUES 176-277
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.75；PEG6000, 100 MM SODIUM CITRATE PH 4.75
|
Resolution 1.70 Å R-free 0.208 |
| 2CJY Extended substrate recognition in caspase-3 revealed by high resolution X-ray structure analysis Deposited 2006-04-09 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Fragment：ALPHA SUBUNIT, RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：BETA SUBUNIT, RESIDUES 176-277
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.75；PEG6000, 100 MM SODIUM CITRATE PH 4.75
|
Resolution 1.67 Å R-free 0.206 |
| 2CNK Crystal structures of caspase-3 in complex with aza-peptide epoxide inhibitors. Deposited 2006-05-22 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Fragment：ALPHA SUBUNIT, RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：BETA SUBUNIT, RESIDUES 176-277
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.75；PEG6000, 100 MM SODIUM CITRATE PH 4.75
|
Resolution 1.75 Å R-free 0.193 |
| 2CNL Crystal structures of caspase-3 in complex with aza-peptide epoxide inhibitors. Deposited 2006-05-22 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Fragment：ALPHA SUBUNIT, RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：BETA SUBUNIT, RESIDUES 176-277
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.75；PEG6000, 100 MM SODIUM CITRATE PH 4.75
|
Resolution 1.67 Å R-free 0.217 |
| 2CNN Crystal structures of caspase-3 in complex with aza-peptide epoxide inhibitors. Deposited 2006-05-22 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Fragment：ALPHA SUBUNIT, RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：BETA SUBUNIT
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.75；PEG6000, 100 MM SODIUM CITRATE PH 4.75
|
Resolution 1.70 Å R-free 0.206 |
| 2CNO Crystal structures of caspase-3 in complex with aza-peptide epoxide inhibitors. Deposited 2006-05-22 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Fragment：ALPHA SUBUNIT, RESIDUES 29-175
Chain B
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.75；PEG6000, 100 MM SODIUM CITRATE PH 4.75
|
Resolution 1.95 Å R-free 0.198 |
| 2DKO Extended substrate recognition in caspase-3 revealed by high resolution X-ray structure analysis Deposited 2006-04-12 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–174（146 aa）
Fragment：Caspase-3 p17 subunit, residues 29-174
Chain B
175–277（103 aa）
Fragment：Caspase-3 p12 subunit, residues 175-277
|
Mutation：D175A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 4.75；293 K；pH 4.75, VAPOR DIFFUSION, temperature 293K
|
Resolution 1.06 Å R-free 0.175 |
| 2H5I Crystal structure of caspase-3 with inhibitor Ac-DEVD-Cho Deposited 2006-05-26 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–174（146 aa）
Fragment：residues 29-174
Chain B
184–277（94 aa）
Fragment：residues 184-277
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol and 14-18% PEG 6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.69 Å R-free 0.227 |
| 2H5J Crystal strusture of caspase-3 with inhibitor Ac-DMQD-Cho Deposited 2006-05-26 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–174（146 aa）
Fragment：residues 29-174
Chain B
184–277（94 aa）
Fragment：residues 184-277
Chain C
29–174（146 aa）
Fragment：residues 29-174
Chain D
184–277（94 aa）
Fragment：residues 184-277
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol and 14-18% PEG 6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.269 |
| 2H65 Crystal strusture of caspase-3 with inhibitor Ac-VDVAD-Cho Deposited 2006-05-30 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–174（146 aa）
Fragment：residues 29-174
Chain B
184–277（94 aa）
Fragment：residues 184-277
Chain C
29–174（146 aa）
Fragment：residues 29-174
Chain D
184–277（94 aa）
Fragment：residues 184-277
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol and 14-18% PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.30 Å R-free 0.246 |
| 2J30 The Role of Loop Bundle Hydrogen Bonds in the Maturation and Activity of (Pro)caspase-3 Deposited 2006-08-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
29–277（249 aa）
Fragment：RESIDUES 29-277
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL, PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE. THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS. THE IDEAL FREEZING CONDITIONS WERE FOUND TO BE WITH 80% MOTHER LIQUOR AND 20% PEG 400.
|
Resolution 1.40 Å R-free 0.207 |
| 2J31 The Role of Loop Bundle Hydrogen Bonds in the Maturation and Activity of(Pro)caspase-3 Deposited 2006-08-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
29–277（249 aa）
Fragment：RESIDUES 29-277
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；8 MG/ML PRO-CASPASE3 IN 10 MM TRIS- HCL, PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE. THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW WITHIN THREE DAYS FOR WILD-TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS. THE IDEAL FREEZING CONDITIONS WERE FOUND TO BE WITH 80% MOTHER LIQUOR AND 20% PEG 400.
|
Resolution 1.50 Å R-free 0.216 |
| 2J32 The Role of Loop Bundle Hydrogen Bonds in the Maturation and Activity of(Pro)caspase-3 Deposited 2006-08-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
29–277（249 aa）
Fragment：RESIDUES 29-277
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；8 MG/ML PRO-CASPASE3 IN 10 MM TRIS- HCL, PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE. THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW WITHIN THREE DAYS FOR WILD-TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS. THE IDEAL FREEZING CONDITIONS WERE FOUND TO BE WITH 80% MOTHER LIQUOR AND 20% PEG 400.
|
Resolution 1.30 Å R-free 0.202 |
| 2J33 The Role of Loop Bundle Hydrogen Bonds in the Maturation and Activity of (Pro)caspase-3 Deposited 2006-08-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
29–277（249 aa）
Fragment：RESIDUES 29-277
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL, PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE. THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS. THE IDEAL FREEZING CONDITIONS WERE FOUND TO BE WITH 80% MOTHER LIQUOR AND 20% PEG 400.
|
Resolution 2.00 Å R-free 0.205 |
| 2XYG Caspase-3:CAS329306 Deposited 2010-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–174（146 aa）
Fragment：RESIDUES 29-174
Chain B
185–277（93 aa）
Fragment：RESIDUES 185-277
|
Not recorded | TQ8 N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
15% PEG6000, 0.1M SODIUM CITRATE, PH 5.0
|
Resolution 1.54 Å R-free 0.197 |
| 2XYH Caspase-3:CAS60254719 Deposited 2010-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–174（146 aa）
Fragment：RESIDUES 29-174
Chain B
185–277（93 aa）
Fragment：RESIDUES 185-277
|
Not recorded | TQ9 5-CHLORO-4-OXOPENTANOIC ACID × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.89 Å R-free 0.215 |
| 2XYP Caspase-3:CAS26049945 Deposited 2010-11-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–174（146 aa）
Fragment：RESIDUES 29-174
Chain B
185–277（93 aa）
Fragment：RESIDUES 185-277
|
Not recorded | XVE PHENYLMETHYL N-[(2S)-4-CHLORO-3-OXO-1-PHENYL-BUTAN-2-YL]CARBAMATE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.86 Å R-free 0.204 |
| 2XZD Caspase-3 in Complex with an Inhibitory DARPin-3.4 Deposited 2010-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
27–175（149 aa）
Fragment：P17 SUBUNIT, RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：P12 SUBUNIT, RESIDUES 176-277
|
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) | MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；100 MM HEPES, PH 7.3 (RT), 40 % 2-METHYL-2,4-PENTANEDIOL.
|
Resolution 2.10 Å R-free 0.218 |
| 2XZD Caspase-3 in Complex with an Inhibitory DARPin-3.4 Deposited 2010-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
27–175（149 aa）
Fragment：P17 SUBUNIT, RESIDUES 29-175
Chain D
176–277（102 aa）
Fragment：P12 SUBUNIT, RESIDUES 176-277
|
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) | MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；100 MM HEPES, PH 7.3 (RT), 40 % 2-METHYL-2,4-PENTANEDIOL.
|
Resolution 2.10 Å R-free 0.218 |
| 2XZT Caspase-3 in Complex with DARPin-3.4_I78S Deposited 2010-11-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
29–175（147 aa）
Fragment：P17 SUBUNIT, RESIDUES 29-175
Chain D
176–277（102 aa）
Fragment：P12 SUBUNIT, RESIDUES 176-277
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.8；100 MM HEPES, PH 7.8 (RT) 70 % 2-METHYL-2,4-PENTANEDIOL
|
Resolution 2.70 Å R-free 0.231 |
| 2XZT Caspase-3 in Complex with DARPin-3.4_I78S Deposited 2010-11-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
29–175（147 aa）
Fragment：P17 SUBUNIT, RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：P12 SUBUNIT, RESIDUES 176-277
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.8；100 MM HEPES, PH 7.8 (RT) 70 % 2-METHYL-2,4-PENTANEDIOL
|
Resolution 2.70 Å R-free 0.231 |
| 2Y0B Caspase-3 in Complex with an Inhibitory DARPin-3.4_S76R Deposited 2010-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；100 MM HEPES, PH 7.3 (RT) 40 % 2-METHYL-2,4-PENTANEDIOL
|
Resolution 2.10 Å R-free 0.217 |
| 2Y0B Caspase-3 in Complex with an Inhibitory DARPin-3.4_S76R Deposited 2010-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
29–175（147 aa）
Chain D
176–277（102 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.3；100 MM HEPES, PH 7.3 (RT) 40 % 2-METHYL-2,4-PENTANEDIOL
|
Resolution 2.10 Å R-free 0.217 |
| 3DEH Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors Deposited 2008-06-10 | 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
29–277（249 aa）
Chain B
29–277（249 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) 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, HANGING DROP；pH 7.4；277 K；4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.50 Å R-free 0.268 |
| 3DEH Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors Deposited 2008-06-10 | 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 C
29–277（249 aa）
Chain D
29–277（249 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | RXA isoquinoline-1,3,4(2H)-trione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.50 Å R-free 0.268 |
| 3DEH Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors Deposited 2008-06-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–277（249 aa）
Chain B
29–277（249 aa）
Chain C
29–277（249 aa）
Chain D
29–277（249 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | RXA isoquinoline-1,3,4(2H)-trione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.50 Å R-free 0.268 |
| 3DEI Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors Deposited 2008-06-10 | 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
29–277（249 aa）
Chain B
29–277（249 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) 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, HANGING DROP；pH 7.4；277 K；4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.291 |
| 3DEI Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors Deposited 2008-06-10 | 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 C
29–277（249 aa）
Chain D
29–277（249 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | RXB (1S)-2-oxo-1-phenyl-2-[(1,3,4-trioxo-1,2,3,4-tetrahydroisoquinolin-5-yl)amino]ethyl acetate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.291 |
| 3DEI Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors Deposited 2008-06-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–277（249 aa）
Chain B
29–277（249 aa）
Chain C
29–277（249 aa）
Chain D
29–277（249 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | RXB (1S)-2-oxo-1-phenyl-2-[(1,3,4-trioxo-1,2,3,4-tetrahydroisoquinolin-5-yl)amino]ethyl acetate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.291 |
| 3DEJ Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors Deposited 2008-06-10 | 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
29–277（249 aa）
Chain B
29–277（249 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) 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, HANGING DROP；pH 7.4；277 K；4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.60 Å R-free 0.274 |
| 3DEJ Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors Deposited 2008-06-10 | 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 C
29–277（249 aa）
Chain D
29–277（249 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | RXC (1S)-1-(3-chlorophenyl)-2-oxo-2-[(1,3,4-trioxo-1,2,3,4-tetrahydroisoquinolin-5-yl)amino]ethyl acetate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.60 Å R-free 0.274 |
| 3DEJ Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors Deposited 2008-06-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–277（249 aa）
Chain B
29–277（249 aa）
Chain C
29–277（249 aa）
Chain D
29–277（249 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | RXC (1S)-1-(3-chlorophenyl)-2-oxo-2-[(1,3,4-trioxo-1,2,3,4-tetrahydroisoquinolin-5-yl)amino]ethyl acetate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.60 Å R-free 0.274 |
| 3DEK Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors Deposited 2008-06-10 | 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
29–277（249 aa）
Chain B
29–277（249 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | RXD N-[3-(2-fluoroethoxy)phenyl]-N'-(1,3,4-trioxo-1,2,3,4-tetrahydroisoquinolin-6-yl)butanediamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.40 Å R-free 0.253 |
| 3DEK Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors Deposited 2008-06-10 | 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
29–277（249 aa）
Chain D
29–277（249 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) 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, HANGING DROP；pH 7.4；277 K；4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.40 Å R-free 0.253 |
| 3DEK Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors Deposited 2008-06-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–277（249 aa）
Chain B
29–277（249 aa）
Chain C
29–277（249 aa）
Chain D
29–277（249 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | RXD N-[3-(2-fluoroethoxy)phenyl]-N'-(1,3,4-trioxo-1,2,3,4-tetrahydroisoquinolin-6-yl)butanediamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.40 Å R-free 0.253 |
| 3EDQ Crystal structure of Caspase-3 with inhibitor AC-LDESD-CHO Deposited 2008-09-03 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Fragment：UNP RESIDUES 29-175
Chain B
176–277（102 aa）
Fragment：UNP RESIDUES 176-283
Chain C
29–175（147 aa）
Fragment：UNP RESIDUES 29-175
Chain D
176–277（102 aa）
Fragment：UNP RESIDUES 176-283
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 MM SODIUM CITRATE, 5% GLYCEROL, 10 MM DITHIOTHREITOL AND 14-18% PEG6000, PH 7.0., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 1.61 Å R-free 0.223 |
| 3GJQ Caspase-3 Binds Diverse P4 Residues in Peptides Deposited 2009-03-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol, 14-18% PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.60 Å R-free 0.290 |
| 3GJQ Caspase-3 Binds Diverse P4 Residues in Peptides Deposited 2009-03-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
29–175（147 aa）
Chain D
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol, 14-18% PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.60 Å R-free 0.290 |
| 3GJR Caspase-3 Binds Diverse P4 Residues in Peptides Deposited 2009-03-09 | Different construct 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
29–175（147 aa）
Chain B
176–277（102 aa）
|
Not recorded | DZE methyl (3S)-3-[(tert-butoxycarbonyl)amino]-4-oxopentanoate × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol, 14-18% PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.20 Å R-free 0.253 |
| 3GJR Caspase-3 Binds Diverse P4 Residues in Peptides Deposited 2009-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
29–175（147 aa）
Chain D
176–277（102 aa）
|
Not recorded | DZE methyl (3S)-3-[(tert-butoxycarbonyl)amino]-4-oxopentanoate × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol, 14-18% PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.20 Å R-free 0.253 |
| 3GJS Caspase-3 Binds Diverse P4 Residues in Peptides Deposited 2009-03-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol, 14-18% PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.90 Å R-free 0.248 |
| 3GJS Caspase-3 Binds Diverse P4 Residues in Peptides Deposited 2009-03-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
29–175（147 aa）
Chain D
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol, 14-18% PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.90 Å R-free 0.248 |
| 3GJT Caspase-3 Binds Diverse P4 Residues in Peptides Deposited 2009-03-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol, 14-18% PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.20 Å R-free 0.288 |
| 3GJT Caspase-3 Binds Diverse P4 Residues in Peptides Deposited 2009-03-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
29–175（147 aa）
Chain D
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol, 14-18% PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.20 Å R-free 0.288 |
| 3H0E 3,4-Dihydropyrimido(1,2-a)indol-10(2H)-ones as Potent Non-Peptidic Inhibitors of Caspase-3 Deposited 2009-04-09 | Different construct 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
29–277（249 aa）
Fragment：Subunits p17 and p12
Chain B
29–277（249 aa）
Fragment：Subunits p17 and p12
|
Not recorded | H0E (10S)-3,3-dimethyl-8-{[(2S)-2-(phenoxymethyl)pyrrolidin-1-yl]sulfonyl}-2,3,4,10-tetrahydropyrimido[1,2-a]indol-10-ol × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；298 K；0.1M NaCitrate, pH 5.9, 10mM L-Cys, 5% Glycerol, 10% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.200 |
| 3ITN Crystal structure of Pseudo-activated Procaspase-3 Deposited 2009-08-28 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
29–277（249 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291.15 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl (pH 8.5) and 1 mM DTT. The protein was concentrated to 10 mg/mL using Amicon ultrafree centrifugal filter devices, and inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl (pH 8.5), concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl (pH 8.5), 10 mM DTT, and 3 mM NaN3. Crystals were obtained by the hanging drop vapor diffusion method. Concentrated protein (2 L) was mixed 1:1 with a reservoir solution that contained 100 mM sodium citrate (pH 5), 3 mM NaN3, 10 mM DTT, and 17% PEG 6000 (w/v). The crystallization plates were incubated at 18 C., VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
|
Resolution 1.63 Å R-free 0.224 |
| 3ITN Crystal structure of Pseudo-activated Procaspase-3 Deposited 2009-08-28 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–277（249 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291.15 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl (pH 8.5) and 1 mM DTT. The protein was concentrated to 10 mg/mL using Amicon ultrafree centrifugal filter devices, and inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl (pH 8.5), concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl (pH 8.5), 10 mM DTT, and 3 mM NaN3. Crystals were obtained by the hanging drop vapor diffusion method. Concentrated protein (2 L) was mixed 1:1 with a reservoir solution that contained 100 mM sodium citrate (pH 5), 3 mM NaN3, 10 mM DTT, and 17% PEG 6000 (w/v). The crystallization plates were incubated at 18 C., VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
|
Resolution 1.63 Å R-free 0.224 |
| 3ITN Crystal structure of Pseudo-activated Procaspase-3 Deposited 2009-08-28 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
29–277（249 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291.15 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl (pH 8.5) and 1 mM DTT. The protein was concentrated to 10 mg/mL using Amicon ultrafree centrifugal filter devices, and inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl (pH 8.5), concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl (pH 8.5), 10 mM DTT, and 3 mM NaN3. Crystals were obtained by the hanging drop vapor diffusion method. Concentrated protein (2 L) was mixed 1:1 with a reservoir solution that contained 100 mM sodium citrate (pH 5), 3 mM NaN3, 10 mM DTT, and 17% PEG 6000 (w/v). The crystallization plates were incubated at 18 C., VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
|
Resolution 1.63 Å R-free 0.224 |
| 3KJF Caspase 3 Bound to a covalent inhibitor Deposited 2009-11-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
|
Not recorded | B92 (3S)-3-({[(5S,10aS)-2-{(2S)-4-carboxy-2-[(phenylacetyl)amino]butyl}-1,3-dioxo-2,3,5,7,8,9,10,10a-octahydro-1H-[1,2,4]triazolo[1,2-a]cinnolin-5-yl]carbonyl}amino)-4-oxopentanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.8；277 K；Inhibitor (2 microliters of a 100 mM DMSO stock) added to 100 microliters of protein (6.5 mg/mL) in 20 mM Tris, 10 mM DTT pH 8.0. Drops contained equal volumes of protein and well solution (16% ethanol, 0.1 M Tris pH 7.8), VAPOR DIFFUSION, temperature 277K
|
Resolution 2.00 Å R-free 0.206 |
| 3PCX Caspase-3 E246A, K242A Double Mutant Deposited 2010-10-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
29–277（249 aa）
Fragment：UNP residues 29-277
|
Mutation：E246A, K242A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；300 K；Inhibitor, Ac-DEVD-CMK, reconstituted in DMSO, was added at a 5:1 inhibitor:protein ratio (w/w). Final buffer consisted of 10 mM Tris-HCl, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING DROP, pH 8.5, temperature 300K
|
Resolution 1.50 Å R-free 0.213 |
| 3PCX Caspase-3 E246A, K242A Double Mutant Deposited 2010-10-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
29–277（249 aa）
Fragment：UNP residues 29-277
|
Mutation：E246A, K242A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；300 K；Inhibitor, Ac-DEVD-CMK, reconstituted in DMSO, was added at a 5:1 inhibitor:protein ratio (w/w). Final buffer consisted of 10 mM Tris-HCl, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING DROP, pH 8.5, temperature 300K
|
Resolution 1.50 Å R-free 0.213 |
| 3PCX Caspase-3 E246A, K242A Double Mutant Deposited 2010-10-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
29–277（249 aa）
Fragment：UNP residues 29-277
|
Mutation：E246A, K242A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；300 K；Inhibitor, Ac-DEVD-CMK, reconstituted in DMSO, was added at a 5:1 inhibitor:protein ratio (w/w). Final buffer consisted of 10 mM Tris-HCl, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING DROP, pH 8.5, temperature 300K
|
Resolution 1.50 Å R-free 0.213 |
| 3PD0 Caspase-3 E246A Deposited 2010-10-22 | 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
29–277（249 aa）
Fragment：UNP residues 29-277
|
Mutation：E246A | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Inhibitor, Ac-DEVD-CMK, reconstituted in DMSO, was added at a 5:1 inhibitor:protein ratio (w/w). Final buffer consisted of 10 mM Tris-HCl, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING DROP, pH 8.5, temperature 291K
|
Resolution 2.00 Å R-free 0.204 |
| 3PD0 Caspase-3 E246A Deposited 2010-10-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
29–277（249 aa）
Fragment：UNP residues 29-277
|
Mutation：E246A | CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Inhibitor, Ac-DEVD-CMK, reconstituted in DMSO, was added at a 5:1 inhibitor:protein ratio (w/w). Final buffer consisted of 10 mM Tris-HCl, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING DROP, pH 8.5, temperature 291K
|
Resolution 2.00 Å R-free 0.204 |
| 3PD1 Caspase-3 K242A Deposited 2010-10-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
29–277（249 aa）
Fragment：UNP residues 29-277
|
Mutation：K242A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Inhibitor, Ac-DEVD-CMK, reconstituted in DMSO, was added at a 5:1 inhibitor:protein ratio (w/w). Final buffer consisted of 10 mM Tris-HCl (pH 8.5), 10 mM DTT, 3 mM NaN3., VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.62 Å R-free 0.226 |
| 3PD1 Caspase-3 K242A Deposited 2010-10-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
29–277（249 aa）
Fragment：UNP residues 29-277
|
Mutation：K242A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Inhibitor, Ac-DEVD-CMK, reconstituted in DMSO, was added at a 5:1 inhibitor:protein ratio (w/w). Final buffer consisted of 10 mM Tris-HCl (pH 8.5), 10 mM DTT, 3 mM NaN3., VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.62 Å R-free 0.226 |
| 3PD1 Caspase-3 K242A Deposited 2010-10-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
29–277（249 aa）
Fragment：UNP residues 29-277
|
Mutation：K242A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Inhibitor, Ac-DEVD-CMK, reconstituted in DMSO, was added at a 5:1 inhibitor:protein ratio (w/w). Final buffer consisted of 10 mM Tris-HCl (pH 8.5), 10 mM DTT, 3 mM NaN3., VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.62 Å R-free 0.226 |
| 4DCJ Crystal structure of caspase 3, L168D mutant Deposited 2012-01-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
|
Mutation：L168D | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 6000, 100mM sodium citrate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.70 Å R-free 0.213 |
| 4DCJ Crystal structure of caspase 3, L168D mutant Deposited 2012-01-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
29–175（147 aa）
Chain E
176–277（102 aa）
|
Mutation：L168D | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 6000, 100mM sodium citrate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.70 Å R-free 0.213 |
| 4DCO Crystal Structure of caspase 3, L168Y mutant Deposited 2012-01-18 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
|
Mutation：L168Y/L1168Y | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 6000, 100mM sodium citrate pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.70 Å R-free 0.216 |
| 4DCO Crystal Structure of caspase 3, L168Y mutant Deposited 2012-01-18 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
29–175（147 aa）
Chain E
176–277（102 aa）
|
Mutation：L168Y/L1168Y | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 6000, 100mM sodium citrate pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.70 Å R-free 0.216 |
| 4DCP Crystal Structure of caspase 3, L168F mutant Deposited 2012-01-18 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
|
Mutation：L168F/L1168F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 6000, 100mM sodium citrate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.70 Å R-free 0.218 |
| 4DCP Crystal Structure of caspase 3, L168F mutant Deposited 2012-01-18 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
29–175（147 aa）
Chain E
176–277（102 aa）
|
Mutation：L168F/L1168F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 6000, 100mM sodium citrate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.70 Å R-free 0.218 |
| 4EHA Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–277（277 aa）
Fragment：Caspase-2
|
Mutation：V266H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% -16% PEG 6000. Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.70 Å R-free 0.233 |
| 4EHA Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–277（277 aa）
Fragment：Caspase-2
|
Mutation：V266H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% -16% PEG 6000. Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.70 Å R-free 0.233 |
| 4EHA Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Fragment：Caspase-2
Chain C
1–277（277 aa）
Fragment：Caspase-2
|
Mutation：V266H Mutation：V266H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% -16% PEG 6000. Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.70 Å R-free 0.233 |
| 4EHD Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–277（277 aa）
|
Mutation：Y197C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000. Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.58 Å R-free 0.199 |
| 4EHD Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–277（277 aa）
|
Mutation：Y197C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000. Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.58 Å R-free 0.199 |
| 4EHF Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–277（277 aa）
|
Mutation：Y197C,V266H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000. Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.66 Å R-free 0.185 |
| 4EHF Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–277（277 aa）
|
Mutation：Y197C,V266H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000. Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.66 Å R-free 0.185 |
| 4EHH Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–277（277 aa）
|
Mutation：E124A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000. Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.78 Å R-free 0.281 |
| 4EHH Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：E124A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000. Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.78 Å R-free 0.281 |
| 4EHK Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–277（277 aa）
|
Mutation：E124A,Y197C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000. Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.67 Å R-free 0.230 |
| 4EHK Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–277（277 aa）
|
Mutation：E124A,Y197C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000. Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.67 Å R-free 0.230 |
| 4EHK Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Mutation：E124A,Y197C Mutation：E124A,Y197C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000. Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.67 Å R-free 0.230 |
| 4EHL Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–277（277 aa）
|
Mutation：E124A,V266H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3.
Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000.
Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.80 Å R-free 0.208 |
| 4EHL Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–277（277 aa）
|
Mutation：E124A,V266H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3.
Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000.
Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.80 Å R-free 0.208 |
| 4EHL Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Mutation：E124A,V266H Mutation：E124A,V266H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Protein solution: 8 mg/ml protein in 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3.
Reservoir solution: 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000.
Drop: 4ul protein Solution: 4 ul reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.80 Å R-free 0.208 |
| 4EHN Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–277（277 aa）
|
Mutation：E124A,Y197C,V266H | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.69 Å R-free 0.192 |
| 4EHN Allosteric Modulation of Caspase-3 through Mutagenesis Deposited 2012-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：E124A,Y197C,V266H | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.69 Å R-free 0.192 |
| 4JJE Caspase-3 specific unnatural amino acid peptides Deposited 2013-03-07 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
29–277（249 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.05M Sodium citrate pH 5.5, 14% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 1.48 Å R-free 0.174 |
| 4JQY Human procaspase-3, crystal form 1 Deposited 2013-03-20 | 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
34–277（244 aa）
Fragment：protease domain (UNP residues 34-277)
Chain B
34–277（244 aa）
Fragment：protease domain (UNP residues 34-277)
|
Mutation：C163A Mutation：C163A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；10 mM Tris, pH 8.0, 10 mM DTT, 50 mM sodium chloride, 10% PEG3350, 200 mM ammonium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.243 |
| 4JQZ Human procaspase-3, crystal form 2 Deposited 2013-03-20 | 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
34–277（244 aa）
Fragment：protease domain (UNP residues 34-277)
Chain B
34–277（244 aa）
Fragment：protease domain (UNP residues 34-277)
|
Mutation：C163A Mutation：C163A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.9；291 K；10 mM Tris, pH 8.0, 10 mM DTT, 50 mM sodium chloride, 16% PEG3350, 150 mM ammonium citrate, pH 4.9, 1 mM 1541 derivative, 5% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.89 Å R-free 0.257 |
| 4JR0 Human procaspase-3 bound to Ac-DEVD-CMK Deposited 2013-03-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
34–277（244 aa）
Fragment：protease domain (UNP residues 34-277)
Chain B
34–277（244 aa）
Fragment：protease domain (UNP residues 34-277)
|
Mutation：D175A Mutation：D175A | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；10 mM Tris, pH 8.0, 10 mM DTT, 50 mM sodium chloride, 10% PEG3350, 250 mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.80 Å R-free 0.195 |
| 4PRY Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–277（277 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M Sodium citrate, pH 5.5, 12% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 1.70 Å R-free 0.187 |
| 4PS0 Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–277（277 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.15 M sodium citrate, pH 5.5, 14% PEG 6000, 0.3% sodium azide, 0.01 M DTT, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 1.63 Å R-free 0.179 |
| 4PS0 Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–277（277 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.15 M sodium citrate, pH 5.5, 14% PEG 6000, 0.3% sodium azide, 0.01 M DTT, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 1.63 Å R-free 0.179 |
| 4QTX Caspase-3 Y195A Deposited 2014-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：Y195A | ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 L drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.97 Å R-free 0.259 |
| 4QTY Caspase-3 E190A Deposited 2014-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
29–277（249 aa）
|
Mutation：E190A | NA SODIUM ION × 2 AZI AZIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 L drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.60 Å R-free 0.195 |
| 4QU0 Caspase-3 Y195AV266H Deposited 2014-07-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：Y195A V266H | AZI AZIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 L drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.95 Å R-free 0.183 |
| 4QU5 Caspase-3 T140V Deposited 2014-07-10 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：T140V | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 L drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.91 Å R-free 0.254 |
| 4QU8 Caspase-3 M61A V266H Deposited 2014-07-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：M61A V266H | CL CHLORIDE ION × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 L drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.72 Å R-free 0.191 |
| 4QU9 Caspase-3 F128A Deposited 2014-07-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：F128A | AZI AZIDE ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 L drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.56 Å R-free 0.169 |
| 4QUA Caspase-3 Y195F Deposited 2014-07-10 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：Y195F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 L drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.89 Å R-free 0.254 |
| 4QUB Caspase-3 K137A Deposited 2014-07-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：K137A | AZI AZIDE ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 L drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.69 Å R-free 0.189 |
| 4QUD Caspase-3 T140F Deposited 2014-07-10 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain B
1–277（277 aa）
|
Mutation：T140F Mutation：T140F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4uL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.00 Å R-free 0.284 |
| 4QUE Caspase-3 Y195FV266H Deposited 2014-07-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Mutation：Y195F V266H Mutation：Y195F V266H | DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 AZI AZIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 uL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.84 Å R-free 0.223 |
| 4QUG Caspase-3 M61A Deposited 2014-07-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Mutation：M61A Mutation：M61A | CL CHLORIDE ION × 1 ACT ACETATE ION × 1 AZI AZIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291 K by the hanging drop vapor diffusion method using 4 uL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants. , VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.92 Å R-free 0.189 |
| 4QUH Caspase-3 T140G Deposited 2014-07-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Mutation：T140G Mutation：T140G | MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 AZI AZIDE ION × 4 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291 by the hanging drop vapor diffusion method using 4 L drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.76 Å R-free 0.187 |
| 4QUI Caspase-3 F128AV266H Deposited 2014-07-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain B
1–277（277 aa）
|
Mutation：F128A, V266H Mutation：F128A, V266H | DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 18 oC by the hanging drop vapor diffusion method using 4 uL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.76 Å R-free 0.193 |
| 4QUI Caspase-3 F128AV266H Deposited 2014-07-10 | 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
1–277（277 aa）
Chain B
1–277（277 aa）
|
Mutation：F128A, V266H Mutation：F128A, V266H | DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 18 oC by the hanging drop vapor diffusion method using 4 uL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.76 Å R-free 0.193 |
| 4QUJ Caspase-3 T140GV266H Deposited 2014-07-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：T140G V266H | NA SODIUM ION × 2 AZI AZIDE ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 L drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.50 Å R-free 0.183 |
| 4QUL Caspase-3 F55W Deposited 2014-07-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Mutation：F55W Mutation：F55W | AZI AZIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 uL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.90 Å R-free 0.258 |
| 5I9B Caspase 3 V266A Deposited 2016-02-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：V266A | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 1.80 Å R-free 0.204 |
| 5I9T Caspase 3 V266C Deposited 2016-02-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Mutation：V266C Mutation：V266C | ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 1.95 Å R-free 0.198 |
| 5IAB Caspase 3 V266D Deposited 2016-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Mutation：V266D Mutation：V266D | DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 1.79 Å R-free 0.213 |
| 5IAE Caspase 3 V266F Deposited 2016-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Mutation：V266F Mutation：V266F | CL CHLORIDE ION × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 1.55 Å R-free 0.182 |
| 5IAG Caspase 3 V266Q Deposited 2016-02-21 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–277（277 aa）
|
Mutation：V266Q | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 1.98 Å R-free 0.216 |
| 5IAJ Caspase 3 V266L Deposited 2016-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：V266L | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 1.58 Å R-free 0.203 |
| 5IAK Caspase 3 V266S Deposited 2016-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：V266S | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 1.82 Å R-free 0.199 |
| 5IAN Caspase 3 V266N Deposited 2016-02-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–277（277 aa）
|
Mutation：V266N | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 2.70 Å R-free 0.247 |
| 5IAR Caspase 3 V266W Deposited 2016-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：V266W | NA SODIUM ION × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 1.76 Å R-free 0.185 |
| 5IAS Caspase 3 V266Y Deposited 2016-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：V266Y | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 1.54 Å R-free 0.189 |
| 5IBC Caspase 3 V266I Deposited 2016-02-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：V266I | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 1.66 Å R-free 0.208 |
| 5IBP Caspase 3 V266M Deposited 2016-02-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
|
Mutation：V266M | AZI AZIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 1.38 Å R-free 0.174 |
| 5IBR Caspase 3 V266K Deposited 2016-02-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Mutation：V266K Mutation：V266K | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Caspase-3 variants were crystallized in the presence of
Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL,
PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON
ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK
RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE.
THE PROTEIN WAS DILUTED TO A CONCENTRATION OF 8 MG/ML BY ADDING 10 MM
TRIS-HCL, PH 8.5, CONCENTRATED DTT AND CONCENTRATED NAN3 SO THAT THE
FINAL BUFFER WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF
CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM
SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS
WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW
WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.
|
Resolution 1.74 Å R-free 0.202 |
| 5IC4 Crystal structure of caspase-3 DEVE peptide complex Deposited 2016-02-22 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–175（175 aa）
Chain B
176–276（101 aa）
Chain C
1–175（175 aa）
Chain D
176–276（101 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；60% (v/v) tacsimate pH 7
|
Resolution 2.65 Å R-free 0.239 |
| 5IC4 Crystal structure of caspase-3 DEVE peptide complex Deposited 2016-02-22 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain E
1–175（175 aa）
Chain F
176–276（101 aa）
Chain G
1–175（175 aa）
Chain H
176–276（101 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；60% (v/v) tacsimate pH 7
|
Resolution 2.65 Å R-free 0.239 |
| 6BDV Crystal structure of Caspase 3 S150A Deposited 2017-10-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Fragment：UNP residues 1-175
Chain B
176–277（102 aa）
|
Mutation：S150A Mutation：S150A | CL CHLORIDE ION × 1 AZI AZIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.9；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.94 Å R-free 0.196 |
| 6BDV Crystal structure of Caspase 3 S150A Deposited 2017-10-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–175（175 aa）
Fragment：UNP residues 1-175
Chain B
176–277（102 aa）
|
Mutation：S150A Mutation：S150A | CL CHLORIDE ION × 4 AZI AZIDE ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.9；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.94 Å R-free 0.196 |
| 6BDV Crystal structure of Caspase 3 S150A Deposited 2017-10-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–175（175 aa）
Fragment：UNP residues 1-175
Chain B
176–277（102 aa）
|
Mutation：S150A Mutation：S150A | CL CHLORIDE ION × 2 AZI AZIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.9；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.94 Å R-free 0.196 |
| 6BFJ Caspase-3 Mutant - T245D,S249D Deposited 2017-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain B
176–277（102 aa）
|
Mutation：T245D Mutation：S249D | AZI AZIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.54 Å R-free 0.162 |
| 6BFK Caspase-3 Mutant- T245A Deposited 2017-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain C
176–277（102 aa）
|
Mutation：T245A | NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.75 Å R-free 0.180 |
| 6BFK Caspase-3 Mutant- T245A Deposited 2017-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–175（175 aa）
Chain D
176–277（102 aa）
|
Mutation：T245A | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.75 Å R-free 0.180 |
| 6BFL Caspase-3 Mutant- D9A,D28A,T245D Deposited 2017-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain B
176–277（102 aa）
|
Mutation：D9A,D28A Mutation：T245D | AZI AZIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.87 Å R-free 0.190 |
| 6BFO Caspase-3 Mutant- T245D Deposited 2017-10-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain B
176–277（102 aa）
|
Mutation：T245D Mutation：T245D | NA SODIUM ION × 11 AZI AZIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.54 Å R-free 0.174 |
| 6BG0 Caspase-3 Mutant - D9A,D28A,S150D Deposited 2017-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain C
176–277（102 aa）
|
Mutation：D9A,D28A,S150D | NA SODIUM ION × 1 AZI AZIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 2.12 Å R-free 0.201 |
| 6BG0 Caspase-3 Mutant - D9A,D28A,S150D Deposited 2017-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–175（175 aa）
Chain D
176–277（102 aa）
|
Mutation：D9A,D28A,S150D | NA SODIUM ION × 1 AZI AZIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 2.12 Å R-free 0.201 |
| 6BG1 Caspase-3 Mutant - D9A,D28A,S150E Deposited 2017-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain C
176–277（102 aa）
|
Mutation：D9A,D28A,S150E Mutation：D9A,D28A,S150E | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.88 Å R-free 0.193 |
| 6BG4 Caspase-3 Mutant- T152D Deposited 2017-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain E
176–277（102 aa）
|
Mutation：T152D Mutation：T152D | NA SODIUM ION × 5 CL CHLORIDE ION × 1 AZI AZIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.87 Å R-free 0.207 |
| 6BG4 Caspase-3 Mutant- T152D Deposited 2017-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–175（175 aa）
Chain F
176–277（102 aa）
|
Mutation：T152D Mutation：T152D | NA SODIUM ION × 8 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.87 Å R-free 0.207 |
| 6BGK Caspase-3 Mutant- D9A,D28A,T152D Deposited 2017-10-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain C
176–277（102 aa）
|
Mutation：D9A,D28A,T152D | CL CHLORIDE ION × 2 AZI AZIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.87 Å R-free 0.211 |
| 6BGK Caspase-3 Mutant- D9A,D28A,T152D Deposited 2017-10-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–175（175 aa）
Chain D
176–277（102 aa）
|
Mutation：D9A,D28A,T152D | CL CHLORIDE ION × 2 AZI AZIDE ION × 1 NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.87 Å R-free 0.211 |
| 6BGQ Caspase-3 Mutant - S150D Deposited 2017-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain B
176–277（102 aa）
|
Mutation：S150D | CL CHLORIDE ION × 1 AZI AZIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.97 Å R-free 0.224 |
| 6BGQ Caspase-3 Mutant - S150D Deposited 2017-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–175（175 aa）
Chain D
176–277（102 aa）
|
Mutation：S150D | CL CHLORIDE ION × 1 AZI AZIDE ION × 5 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.97 Å R-free 0.224 |
| 6BGR Caspase-3 Mutant - S150E Deposited 2017-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain B
176–277（102 aa）
|
Mutation：S150E | AZI AZIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 2.16 Å R-free 0.234 |
| 6BGS Caspase-3 Mutant - S150Y Deposited 2017-10-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain C
176–277（102 aa）
|
Mutation：S150Y | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.60 Å R-free 0.177 |
| 6BH9 Caspase-3 Mutant - T152A Deposited 2017-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain C
176–277（102 aa）
|
Mutation：T152A | NA SODIUM ION × 3 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.94 Å R-free 0.189 |
| 6BH9 Caspase-3 Mutant - T152A Deposited 2017-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–175（175 aa）
Chain E
176–277（102 aa）
|
Mutation：T152A | NA SODIUM ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.94 Å R-free 0.189 |
| 6BHA Caspase-3 Mutant - T152V Deposited 2017-10-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain B
176–277（102 aa）
|
Mutation：T152V | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
|
Resolution 1.60 Å R-free 0.184 |
| 6CKZ Human caspase-3 in complex with Ac-DW3-KE Deposited 2018-03-01 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain B
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.4；295 K；1:1 dilution with 0.10 M sodium citrate, pH 5.4, 15.2 % PEG6000, 0.010 M DTT, 0.02% NaN3.
|
Resolution 1.50 Å R-free 0.171 |
| 6CL0 Human caspase-3 in complex with Ac-ATS009-KE Deposited 2018-03-01 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–175（175 aa）
Chain B
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；1:1 dilution with 0.10 M sodium citrate, pH 5.0, 13.6 % PEG6000, 0.010 M DTT, 0.02% NaN3
|
Resolution 1.50 Å R-free 0.164 |
| 6X8I Caspase-3 in complex with ketomethylene inhibitor reveals tetrahedral adduct Deposited 2020-06-01 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–175（175 aa）
Fragment：p17 (UNP residues 1-175)
Chain B
1–175（175 aa）
Fragment：p17 (UNP residues 1-175)
Chain C
176–277（102 aa）
Fragment：p12 (UNP residues 176-277)
Chain D
176–277（102 aa）
Fragment：p12 (UNP residues 176-277)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；1:1 protein : 0.10 M sodium citrate, 0.010 M DTT, 0.02% sodium azide, 10% PEG6000
|
Resolution 1.50 Å R-free 0.197 |
| 6X8K Caspase-3 in complex with elongated ketomethylene inhibitor Deposited 2020-06-01 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–175（175 aa）
Fragment：p17 (UNP residues 1-175)
Chain C
176–277（102 aa）
Fragment：p12 (UNP residues 176-277)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；1:1 protein : 0.10 M sodium citrate, 0.010 M DTT, 0.02% sodium azide, 12% PEG6000
|
Resolution 2.17 Å R-free 0.263 |
| 6X8K Caspase-3 in complex with elongated ketomethylene inhibitor Deposited 2020-06-01 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
1–175（175 aa）
Fragment：p17 (UNP residues 1-175)
Chain D
176–277（102 aa）
Fragment：p12 (UNP residues 176-277)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；1:1 protein : 0.10 M sodium citrate, 0.010 M DTT, 0.02% sodium azide, 12% PEG6000
|
Resolution 2.17 Å R-free 0.263 |
| 7RN7 Crystal structure of caspase-3 with inhibitor Ac-VD(Aly)VD-CHO Deposited 2021-07-29 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
34–174（141 aa）
Chain B
184–277（94 aa）
Chain C
34–174（141 aa）
Chain D
184–277（94 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 6000, 5% glycerol, 100 mM sodium citrate pH 6.5, and 10 mM DTT
|
Resolution 2.40 Å R-free 0.252 |
| 7RN8 Crystal structure of caspase-3 with inhibitor Ac-VD(Orn)VD-CHO Deposited 2021-07-29 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
34–174（141 aa）
Chain B
184–277（94 aa）
Chain C
34–174（141 aa）
Chain D
184–277（94 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 6000, 5% glycerol, 100 mM sodium citrate pH 6.5, and 10 mM DTT
|
Resolution 1.88 Å R-free 0.214 |
| 7RN9 Crystal structure of caspase-3 with inhibitor Ac-VDFVD-CHO Deposited 2021-07-29 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
34–174（141 aa）
Chain B
184–277（94 aa）
Chain C
34–174（141 aa）
Chain D
184–277（94 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG 6000, 5% glycerol (v:v), 100 mM sodium citrate pH 5.3, 10 mM DTT, and 30 mM NaN3
|
Resolution 1.67 Å R-free 0.210 |
| 7RNA Crystal structure of caspase-3 with inhibitor Ac-ITV(Dab)D-CHO Deposited 2021-07-29 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
34–174（141 aa）
Chain B
184–277（94 aa）
Chain C
34–174（141 aa）
Chain D
184–277（94 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 6000, 5% glycerol, 100 mM sodium citrate pH 6.5, and 10 mM DTT
|
Resolution 1.90 Å R-free 0.231 |
| 7RNB Crystal structure of caspase-3 with inhibitor Ac-VDRVD-CHO Deposited 2021-07-29 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
34–174（141 aa）
Chain B
184–277（94 aa）
Chain C
34–174（141 aa）
Chain D
184–277（94 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG 6000, 5% glycerol (v:v), 100 mM sodium citrate pH 5.3, 10 mM DTT and 3 mM NaN3
|
Resolution 1.75 Å R-free 0.202 |
| 7RNC Crystal structure of caspase-3 with inhibitor Ac-VDVVD-CHO Deposited 2021-07-29 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
34–174（141 aa）
Chain B
184–277（94 aa）
Chain C
34–174（141 aa）
Chain D
184–277（94 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG 6000, 5% glycerol (v:v), 100 mM sodium citrate pH 5.3, 10 mM DTT, and 30 mM NaN3
|
Resolution 1.93 Å R-free 0.284 |
| 7RND Crystal structure of caspase-3 with inhibitor Ac-VDPVD-CHO Deposited 2021-07-29 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
34–174（141 aa）
Chain B
184–277（94 aa）
Chain C
34–174（141 aa）
Chain D
184–277（94 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 6000, 5% glycerol, 100 mM sodium citrate pH 6.5, and 10 mM DTT
|
Resolution 2.15 Å R-free 0.222 |
| 7RNE Crystal structure of caspase-3 with inhibitor Ac-YKPVD-CHO Deposited 2021-07-29 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
34–174（141 aa）
Chain B
184–277（94 aa）
Chain C
34–174（141 aa）
Chain D
184–277（94 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG 6000, 5% glycerol (v:v), 100 mM sodium citrate pH 5.3, 10 mM DTT, and 30 mM NaN3
|
Resolution 2.73 Å R-free 0.254 |
| 7RNF Crystal structure of caspase-3 with inhibitor Ac-VDKVD-CHO Deposited 2021-07-29 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
34–174（141 aa）
Chain B
184–277（94 aa）
Chain C
34–174（141 aa）
Chain D
184–277（94 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 6000, 5% glycerol, 100 mM sodium citrate pH 6.5, and 10 mM DTT
|
Resolution 2.11 Å R-free 0.237 |
| 7RNG Crystal structure of caspase-3 with inhibitor Ac-ITAKD-CHO Deposited 2021-07-29 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
34–174（141 aa）
Chain B
184–277（94 aa）
Chain C
34–174（141 aa）
Chain D
184–277（94 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG 6000, 5% glycerol (v:v), 100 mM sodium citrate pH 5.3, 10 mM DTT, and 30 mM NaN3
|
Resolution 2.55 Å R-free 0.242 |
| 7SEO Crystal Structure of Caspase-3 with Peptide Inhibitor Ac-VDV(DAB)D-CHO Deposited 2021-09-30 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
29–174（146 aa）
Chain B
184–277（94 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；15% PEG 6000, 5% Glycerol, 100mM Sodium Citrate (pH 5.3), 10mM DTT, 3mM NaN3
|
Resolution 3.25 Å R-free 0.263 |
| 7SEO Crystal Structure of Caspase-3 with Peptide Inhibitor Ac-VDV(DAB)D-CHO Deposited 2021-09-30 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
29–174（146 aa）
Chain D
184–277（94 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；15% PEG 6000, 5% Glycerol, 100mM Sodium Citrate (pH 5.3), 10mM DTT, 3mM NaN3
|
Resolution 3.25 Å R-free 0.263 |
| 7USO Crystal Structure of Caspase-3 with Peptide Inhibitor AcITVKD-CHO Deposited 2022-04-25 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
Chain C
29–175（147 aa）
Chain D
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；15% PEG 6000, 5% Glycerol, 100mM Sodium Citrate (pH 5.3), 10mM DTT, 3mM NaN3
|
Resolution 2.30 Å R-free 0.241 |
| 7USP Crystal Structure of Caspase-3 with Peptide Inhibitor AcITV(Orn)D-CHO Deposited 2022-04-25 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
Chain C
29–175（147 aa）
Chain D
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；14% PEG6000, 5% Glycerol, 100 mM sodium citrate (pH 6.5), 10 mM DTT
|
Resolution 2.85 Å R-free 0.254 |
| 7USQ Crystal Structure of Caspase-3 with Peptide Inhibitor AcDVPD-CHO Deposited 2022-04-25 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
29–175（147 aa）
Chain B
176–277（102 aa）
Chain C
29–175（147 aa）
Chain D
176–277（102 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；14% PEG6000, 5% Glycerol, 100 mM sodium citrate (pH 6.5), 10 mM DTT
|
Resolution 2.71 Å R-free 0.241 |
| 7XN4 Cryo-EM structure of CopC-CaM-caspase-3 with NAD+ Deposited 2022-04-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 7XN5 Cryo-EM structure of CopC-CaM-caspase-3 with ADPR Deposited 2022-04-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Not recorded | NCA NICOTINAMIDE × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.18 Å |
| 7XN6 Cryo-EM structure of CopC-CaM-caspase-3 with ADPR-deacylization Deposited 2022-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–277（277 aa）
Chain C
1–277（277 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | NCA NICOTINAMIDE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.45 Å |
134 other PDB entries and 194 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | ICE3_HUMAN |
| Isoform | — |
| PDB entities | 1, 2 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–147； UniProt 29–175 Author chain B； PDBConstruct 1–102； UniProt 176–277 |
