3ibf

Crystal structure of unliganded caspase-7

Method: X-RAY DIFFRACTION D_max: 69.6 Å Quality: REASONABLE

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

Caspase-7

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 24–196 Chain B； UniProt 207–303 Chain C； UniProt 24–196 Chain D； UniProt 207–303	Fragment：P20 subunit Fragment：P10 subunit	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；2.1M Sodium formate, 0.1M Sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.235

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 3IBF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F1J CRYSTAL STRUCTURE OF CASPASE-7 IN COMPLEX WITH ACETYL-ASP-GLU-VAL-ASP-CHO Deposited 2000-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–303（302 aa） Fragment：P20/P10 CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；30% PEG 4000, 0.1 M Na-citrate, 0.2 M ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.35 Å R-free 0.263
1F1J CRYSTAL STRUCTURE OF CASPASE-7 IN COMPLEX WITH ACETYL-ASP-GLU-VAL-ASP-CHO Deposited 2000-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–303（302 aa） Fragment：P20/P10 CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；30% PEG 4000, 0.1 M Na-citrate, 0.2 M ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.35 Å R-free 0.263
1F1J CRYSTAL STRUCTURE OF CASPASE-7 IN COMPLEX WITH ACETYL-ASP-GLU-VAL-ASP-CHO Deposited 2000-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 2–303（302 aa） Fragment：P20/P10 CATALYTIC DOMAIN Chain B 2–303（302 aa） Fragment：P20/P10 CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；30% PEG 4000, 0.1 M Na-citrate, 0.2 M ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.35 Å R-free 0.263
1F1J CRYSTAL STRUCTURE OF CASPASE-7 IN COMPLEX WITH ACETYL-ASP-GLU-VAL-ASP-CHO Deposited 2000-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–303（302 aa） Fragment：P20/P10 CATALYTIC DOMAIN Chain B 2–303（302 aa） Fragment：P20/P10 CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；30% PEG 4000, 0.1 M Na-citrate, 0.2 M ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.35 Å R-free 0.263
1F1J CRYSTAL STRUCTURE OF CASPASE-7 IN COMPLEX WITH ACETYL-ASP-GLU-VAL-ASP-CHO Deposited 2000-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–303（302 aa） Fragment：P20/P10 CATALYTIC DOMAIN Chain B 2–303（302 aa） Fragment：P20/P10 CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；30% PEG 4000, 0.1 M Na-citrate, 0.2 M ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.35 Å R-free 0.263
1GQF Crystal structure of human procaspase-7 Deposited 2001-11-23	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 47–303（257 aa） Chain B 47–303（257 aa）	Mutation：C187A Mutation：C187A	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；293 K；50 MM MES, PH 5.6, 10 MM MAGNESIUM CHLORIDE, 100 MM AMMONIUM SULFATE, 20% (W/V) PEG 8000	Resolution 2.90 Å R-free 0.285
1I4O CRYSTAL STRUCTURE OF THE XIAP/CASPASE-7 COMPLEX Deposited 2001-02-22	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 24–303（280 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.260
1I4O CRYSTAL STRUCTURE OF THE XIAP/CASPASE-7 COMPLEX Deposited 2001-02-22	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 24–303（280 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.260
1I4O CRYSTAL STRUCTURE OF THE XIAP/CASPASE-7 COMPLEX Deposited 2001-02-22	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 24–303（280 aa） Chain B 24–303（280 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.260
1I51 CRYSTAL STRUCTURE OF CASPASE-7 COMPLEXED WITH XIAP Deposited 2001-02-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 51–198（148 aa） Chain B 199–303（105 aa） Chain C 51–198（148 aa） Chain D 199–303（105 aa）	Mutation：D169A Mutation：D169A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, PEG4000, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.45 Å R-free 0.272
1K86 Crystal structure of caspase-7 Deposited 2001-10-23	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 51–303（253 aa） Chain B 51–303（253 aa）	Mutation：C186A Mutation：C186A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；PEG 4000, sodium chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.60 Å R-free 0.257
1K88 Crystal structure of procaspase-7 Deposited 2001-10-23	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 51–303（253 aa） Fragment：procaspase-7 Chain B 51–303（253 aa） Fragment：procaspase-7	Mutation：C186A Mutation：C186A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；296 K；lithium sulfate, sodium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.70 Å R-free 0.253
1KMC Crystal Structure of the Caspase-7 / XIAP-BIR2 Complex Deposited 2001-12-14	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 1–303（303 aa） Chain B 1–303（303 aa）	Mutation：C285A Mutation：C285A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.3；295 K；PEG 3000, Phosphate/citrate, NaCl, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.90 Å R-free 0.275
1SHJ Caspase-7 in complex with DICA allosteric inhibitor Deposited 2004-02-25	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 50–303（254 aa） Chain B 50–303（254 aa）	Mutation：D169A Mutation：D169A	SO4 SULFATE ION × 3 NXN 2-(2,4-DICHLORO-PHENOXY)-N-(2-MERCAPTO-ETHYL)-ACETAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；citrate, LiSO4, NaCl, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.287
1SHL CASPASE-7 IN COMPLEX WITH FICA ALLOSTERIC INHIBITOR Deposited 2004-02-25	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 57–199（143 aa） Chain A 210–303（94 aa） Chain B 57–199（143 aa） Chain B 210–303（94 aa）	Mutation：D192A Mutation：D192A Mutation：D192A Mutation：D192A	FXN 5-FLUORO-1H-INDOLE-2-CARBOXYLIC ACID-(2-MERCAPTO-ETHYL)-AMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；citrate, lithium sulfate, sodium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.273
2QL5 Crystal Structure of caspase-7 with inhibitor AC-DMQD-CHO Deposited 2007-07-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 24–196（173 aa） Fragment：P20 subunit Chain B 207–303（97 aa） Fragment：P10 subunit Chain C 24–196（173 aa） Fragment：P20 subunit Chain D 207–303（97 aa） Fragment：P10 subunit	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；14.5% PEG 3350, 0.3M diammonium hydrogen citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.34 Å R-free 0.233
2QL7 Crystal Structure of Caspase-7 with inhibitor AC-IEPD-CHO Deposited 2007-07-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 24–196（173 aa） Fragment：P20 subunit Chain B 207–303（97 aa） Fragment：P10 subunit Chain C 24–196（173 aa） Fragment：P20 subunit Chain D 207–303（97 aa） Fragment：P10 subunit	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；298 K；14.5% PEG 3350, 0.3M diammonium hydrogen citrate, 10mM DTT, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.237
2QL9 Crystal Structure of Caspase-7 with inhibitor AC-DQMD-CHO Deposited 2007-07-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 24–196（173 aa） Fragment：P20 subunit Chain B 207–303（97 aa） Fragment：P10 subunit Chain C 24–196（173 aa） Fragment：P20 subunit Chain D 207–303（97 aa） Fragment：P10 subunit	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；298 K；14.5% PEG 3350, 0.3M diammonium hydrogen citrate, 10mM DTT, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.14 Å R-free 0.225
2QLB Crystal Structure of caspase-7 with inhibitor AC-ESMD-CHO Deposited 2007-07-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 24–196（173 aa） Fragment：P20 subunit Chain B 207–303（97 aa） Fragment：P10 subunit Chain C 24–196（173 aa） Fragment：P20 subunit Chain D 207–303（97 aa） Fragment：P10 subunit	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；298 K；14.5% PEG 3350, 0.3M diammonium hydrogen citrate, 10mM DTT, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.25 Å R-free 0.223
2QLF Crystal Structure of Caspase-7 with inhibitor AC-DNLD-CHO Deposited 2007-07-12	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 24–196（173 aa） Fragment：P20 subunit Chain B 207–303（97 aa） Fragment：P10 subunit Chain C 24–196（173 aa） Fragment：P20 subunit Chain D 207–303（97 aa） Fragment：P10 subunit	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；298 K；14.5% PEG 3350, 0.3M diammonium hydrogen citrate, 10mM DTT, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.229
2QLJ Crystal Structure of Caspase-7 with Inhibitor AC-WEHD-CHO Deposited 2007-07-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 24–196（173 aa） Fragment：P20 subunit Chain B 207–303（97 aa） Fragment：P10 subunit Chain C 24–196（173 aa） Fragment：P20 subunit Chain D 207–303（97 aa） Fragment：P10 subunit	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；298 K；14.5% PEG 3350, 0.3M diammonium hydrogen citrate, 10mM DTT, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.234
3EDR The crystal structure of caspase-7 in complex with Acetyl-LDESD-CHO Deposited 2008-09-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 24–196（173 aa） Fragment：P20 subunit (UNP residues 24 to 196) Chain B 207–303（97 aa） Fragment：P10 subunit (UNP residues 207 to 303) Chain C 24–196（173 aa） Fragment：P20 subunit (UNP residues 24 to 196) Chain D 207–303（97 aa） Fragment：P10 subunit (UNP residues 207 to 303)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；2.1M Sodium Formate,0.1M Sodium Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.45 Å R-free 0.248
3H1P Mature Caspase-7 I213A with DEVD-CHO inhibitor bound to active site Deposited 2009-04-13	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 50–303（254 aa） Chain B 50–303（254 aa）	Mutation：I213A Mutation：I213A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；14% PEG 3350, 300mM diammonium hydrogen citrate, 10mM guanidine hydrochloride, and 10mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.61 Å R-free 0.251
3IBC Crystal Structure of Caspase-7 incomplex with Acetyl-YVAD-CHO Deposited 2009-07-15	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 24–196（173 aa） Fragment：P20 subunit Chain B 207–303（97 aa） Fragment：P10 subunit Chain C 24–196（173 aa） Fragment：P20 subunit Chain D 207–303（97 aa） Fragment：P10 subunit	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；14.5% PEG 3350, 0.3 M diammonium hydrogen citrate, 10mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.75 Å R-free 0.242
3R5K A designed redox-controlled caspase-7 Deposited 2011-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–303（303 aa） Chain B 1–303（303 aa）	Mutation：R210C C246S Mutation：R210C C246S	FMT FORMIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；2.1M Formate, 100mM Citrate, 1.25mM Cystamine, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.86 Å R-free 0.251
4FDL Crystal structure of Caspase-7 Deposited 2012-05-28	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 2–303（302 aa） Chain B 2–303（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH 5.0-5.7, 1.9 M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.239
4FEA Crystal structure of CASPASE-7 in Complex with allosteric inhibitor Deposited 2012-05-29	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 57–303（247 aa） Fragment：P20/P10 catalytic domain (UNP residues 57-303) Chain B 57–303（247 aa） Fragment：P20/P10 catalytic domain (UNP residues 57-303)	Not recorded	0TE chloro{methyl hydrogenato(3-)-kappa~2~N,S [pyridin-2-yl(pyridin-2(1H)-ylidene-kappaN)methyl]carbonodithiohydrazonate}copper × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH 5.0-5.7, 1.9 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.79 Å R-free 0.286
4HQ0 Crystal Structure of mutant form of Caspase-7 Deposited 2012-10-25	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 47–303（257 aa） Fragment：UNP residues 47-303 Chain B 47–303（257 aa） Fragment：UNP residues 47-303	Mutation：D198A Mutation：D198A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；sodium acetate pH 4.6, sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.267
4HQR Crystal Structure of mutant form of Caspase-7 Deposited 2012-10-26	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 47–303（257 aa） Fragment：UNP residues 47-303 Chain B 47–303（257 aa） Fragment：UNP residues 47-303	Mutation：D198A Mutation：D198A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；sodium formate, pH 4.6, VAPOR DIFFUSION, temperature 293K	Resolution 3.00 Å R-free 0.253
4JB8 Caspase-7 in Complex with DARPin C7_16 Deposited 2013-02-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 24–198（175 aa） Chain B 207–303（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；293.15 K；0.2M MgCl2, 100mM Tris, 9% PEG 1000, 9% PEG 8000, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 1.70 Å R-free 0.194
4JJ8 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 57–303（247 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；295 K；0.15M Sodium citrate pH 4.0, 2.0 M Sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.94 Å R-free 0.216
4JJ8 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 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 57–303（247 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；295 K；0.15M Sodium citrate pH 4.0, 2.0 M Sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.94 Å R-free 0.216
4JR1 Human procaspase-7 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 57–303（247 aa） Fragment：protease domain (UNP residues 57-303) Chain B 57–303（247 aa） Fragment：protease domain (UNP residues 57-303)	Mutation：D198A Mutation：D198A	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, 2 mM DTT, 50 mM sodium chloride, 200 mM ammonium formate, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.15 Å R-free 0.227
4JR2 Human procaspase-7/caspase-7 heterodimer 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 57–303（247 aa） Fragment：protease domain (UNP residues 57-303) Chain B 57–303（247 aa） Fragment：protease domain (UNP residues 57-303)	Mutation：D198A Mutation：D198A	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；10 mM Tris, pH 8.0, 2 mM DTT, 50 mM sodium chloride, 200 mM sodium/potassium phosphate, 100 mM Bis-Tris propane, pH 6.5, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.65 Å R-free 0.197
4LSZ Caspase-7 in Complex with DARPin D7.18 Deposited 2013-07-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 24–198（175 aa） Fragment：Caspase-7 subunit p20, UNP residues 24-198 Chain B 207–303（97 aa） Fragment：Caspase-7 subunit p10, UNP residues 207-303 Chain C 24–198（175 aa） Fragment：Caspase-7 subunit p20, UNP residues 24-198 Chain D 207–303（97 aa） Fragment：Caspase-7 subunit p10, UNP residues 207-303	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293.15 K；0.8M Sodium Formate, 100mM Tris, 13% PEG 4000, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.26 Å R-free 0.208
4ZVO Caspase-7 Variant 4 (V4) with reprogrammed substrate specificity due to Y230V/W232Y/S234V/Q276D substitutions bound to VEID inhibitor. Deposited 2015-05-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–198（198 aa） Fragment：UNP residues 34-231 Chain B 199–303（105 aa） Fragment：UNP residues 232-336 Chain C 1–198（198 aa） Fragment：UNP residues 34-231 Chain D 199–303（105 aa） Fragment：UNP residues 232-336	Mutation：Y230V, W232Y, S234V, Q276D Mutation：Y230V, W232Y, S234V, Q276D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；300 mM diammonium citrate, 14% PEG 3350, 10 mM GuHCl	Resolution 2.85 Å R-free 0.251
4ZVP Caspase-7 Variant 2 (V2) with reprogrammed substrate specificity due to Y230V/W232M/Q276C substitutions bound to DEVD inhibitor. Deposited 2015-05-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 34–231（198 aa） Fragment：UNP residues 34-231 Chain B 232–336（105 aa） Fragment：UNP residues 232-336 Chain C 34–231（198 aa） Fragment：UNP residues 34-231 Chain D 232–336（105 aa） Fragment：UNP residues 232-336	Mutation：Y230V/W232M/Q276C Mutation：Y230V/W232M/Q276C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；300 mM diammonium citrate, 14% PEG 3350, 10 mM GuHCl, 20% glycerol	Resolution 2.50 Å R-free 0.224
4ZVQ Caspase-7 Variant 2 (V2) with reprogrammed substrate specificity due to Y230V/W232M/Q276C substitutions bound to VEID inhibitor. Deposited 2015-05-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 34–231（198 aa） Fragment：UNP residues 34-231 Chain B 232–336（105 aa） Fragment：UNP residues 232-336 Chain C 34–231（198 aa） Fragment：UNP residues 34-231 Chain D 232–336（105 aa） Fragment：UNP residues 232-336	Mutation：Y230V/W232M/Q276C Mutation：Y230V/W232M/Q276C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；300 mM diammonium citrate, 14% PEG 3350, 10 mM GuHCl, 20% glycerol	Resolution 2.50 Å R-free 0.208
4ZVR Caspase-7 Variant 4 (V4) with reprogrammed substrate specificity due to Y230V/W232Y/S234V/Q276D substitutions bound to DEVD inhibitor. Deposited 2015-05-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–198（198 aa） Fragment：UNP residues 34-231 Chain B 199–303（105 aa） Fragment：UNP residues 232-336 Chain C 1–198（198 aa） Fragment：UNP residues 34-231 Chain D 199–303（105 aa） Fragment：UNP residues 232-336	Mutation：Y230V,W232Y,S234V,Q276D Mutation：Y230V,W232Y,S234V,Q276D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；300 mM diammonium citrate, 14% PEG 3350, 10 mM GuHCl, 20% glycerol	Resolution 2.30 Å R-free 0.224
4ZVS Caspase-7 Variant 1 (V1) with reprogrammed substrate specificity due to Y230A/W232M/S234N substitutions, bound to DEVD inhibitor. Deposited 2015-05-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–198（198 aa） Fragment：UNP residues 34-231 Chain B 199–303（105 aa） Fragment：UNP residues 232-336 Chain C 1–198（198 aa） Fragment：UNP residues 34-231 Chain D 199–303（105 aa） Fragment：UNP residues 232-336	Mutation：Y230A, W232M, S234N Mutation：Y230A, W232M, S234N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277.15 K；300 mM Diammonium Hydrogren Citrate, 14% PEG 3350, 10 mM Guanidinium Chloride, 10 mM Dithiotheritol	Resolution 2.50 Å R-free 0.239
4ZVT Caspase-7 Variant 1 (V1) with reprogrammed substrate specificity due to Y230A/W232M/S234N substitutions, bound to VEID inhibitor. Deposited 2015-05-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–198（198 aa） Fragment：UNP residues 34-231 Chain B 199–303（105 aa） Fragment：UNP residues 232-336 Chain C 1–198（198 aa） Fragment：UNP residues 34-231 Chain D 199–303（105 aa） Fragment：UNP residues 232-336	Mutation：Y230A, W232M, S234N Mutation：Y230A, W232M, S234N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277.15 K；300 mM Diammonium Hydrogen Citrate, 14% PEG 3350, 10 mM Guanidinium Chloride, 10 mM Dithiotheritol	Resolution 2.85 Å R-free 0.234
4ZVU Caspase-7 wild-type bound to the caspase-6 cognate tetrapeptide inhibitor Ac-VEID-cho Deposited 2015-05-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–198（198 aa） Fragment：UNP residues 34-231 Chain B 199–303（105 aa） Fragment：UNP residues 232-336 Chain C 1–198（198 aa） Fragment：UNP residues 34-231 Chain D 199–303（105 aa） Fragment：UNP residues 232-336	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277.15 K；300 mM Diammonium Hydrogen Citrate, 14% PEG 3350, 10 mM Guanidinium Chloride, 10 mM Dithiotheritol	Resolution 2.60 Å R-free 0.252
5IC6 Crystal structure of caspase-7 DEVE peptide complex 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 × 3 PDB declaration: trimeric	Chain A 1–198（198 aa） Chain B 199–303（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2 M ammonium fluoride, 0.1 M sodium acetate pH 4.6, 20% (w/v) PEG 10000	Resolution 2.70 Å R-free 0.241
5IC6 Crystal structure of caspase-7 DEVE peptide complex Deposited 2016-02-22	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 C 1–198（198 aa） Chain D 199–303（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2 M ammonium fluoride, 0.1 M sodium acetate pH 4.6, 20% (w/v) PEG 10000	Resolution 2.70 Å R-free 0.241
5K20 Caspase-7 S239E Phosphomimetic Deposited 2016-05-18	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 34–231（198 aa） Chain B 232–336（105 aa） Chain C 34–231（198 aa） Chain D 232–336（105 aa）	Mutation：S272E Mutation：S272E	FMT FORMIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；2.1 M Sodium Formate 100 mM Sodium Citrate	Resolution 2.20 Å R-free 0.228
5V6U Crystal structure of human caspase-7 soaked with allosteric inhibitor 2-[(2-acetylphenyl)sulfanyl]benzoic acid Deposited 2017-03-17	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 34–336（303 aa） Fragment：UNP residues 34-336 Chain B 34–336（303 aa） Fragment：UNP residues 34-336	Not recorded	8YM 2-[(2-acetylphenyl)sulfanyl]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；295 K；1.9 M sodium formate, 0.1 M sodium citrate, pH 5.7	Resolution 2.80 Å R-free 0.245
5V6Z Crystal structure of human caspase-7 soaked with allosteric inhibitor 2-{[2-(4-chlorophenyl)-2-oxoethyl]sulfanyl}benzoic acid Deposited 2017-03-17	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 34–336（303 aa） Fragment：UNP residues 34-336 Chain B 34–336（303 aa） Fragment：UNP residues 34-336	Not recorded	8YJ 2-{[2-(4-chlorophenyl)-2-oxoethyl]sulfanyl}benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；295 K；1.9 M sodium formate, 0.1 M sodium citrate, pH 5.0-5.7	Resolution 2.60 Å R-free 0.249
6CL1 Caspase-7 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 × 6 PDB declaration: hexameric	Chain A 34–231（198 aa） Chain B 232–336（105 aa） Chain C 34–231（198 aa） Chain D 232–336（105 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 0.15 M sodium citrate, 1.6 M sodium formate, pH 5.0	Resolution 2.65 Å R-free 0.243
6CL2 Caspase-7 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 × 6 PDB declaration: hexameric	Chain A 34–231（198 aa） Chain B 232–336（105 aa） Chain C 34–231（198 aa） Chain D 232–336（105 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 0.15 M sodium citrate, 1.6 M sodium formate, pH 5.0.	Resolution 2.35 Å R-free 0.236
6X8J Caspase-7 in complex with ketomethylene inhibitor reveals tetrahedral adduct Deposited 2020-06-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 34–231（198 aa） Fragment：p20 (UNP residues 34-231) Chain B 34–231（198 aa） Fragment：p20 (UNP residues 34-231) Chain C 232–336（105 aa） Fragment：p11 (UNP residues 232-336) Chain D 232–336（105 aa） Fragment：p11 (UNP residues 232-336)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；295 K；1:1 protein : 0.15 M sodium citrate, 1.4 M sodium formate	Resolution 2.60 Å R-free 0.211
6X8L Caspase-7 in complex with elongated ketomethylene inhibitor Deposited 2020-06-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 34–231（198 aa） Fragment：p20 (UNP residues 34-231) Chain B 34–231（198 aa） Fragment：p20 (UNP residues 34-231) Chain C 232–336（105 aa） Fragment：p11 (UNP residues 232-336) Chain D 232–336（105 aa） Fragment：p11 (UNP residues 232-336)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；1:1 protein : 0.15 M sodium citrate, 1.45 M sodium formate	Resolution 2.45 Å R-free 0.215
7WZS Crystal structure of Chromobacterium violaceum effector CopC in complex with host calmodulin and caspase-7 Deposited 2022-02-19	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 B 24–303（280 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；100 mM Bis-Tris propane pH 7.5, 1.5 M lithium sulfate	Resolution 3.60 Å R-free 0.314
8DGZ Caspase-7 bound to substrate mimic and allosteric inhibitor Deposited 2022-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–303（302 aa） Chain B 2–303（302 aa）	Not recorded	8YJ 2-{[2-(4-chlorophenyl)-2-oxoethyl]sulfanyl}benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；0.1 M sodium citrate and 2.1 M sodium formate	Resolution 2.80 Å R-free 0.254
8DJ3 Caspase-7 bound to novel allosteric inhibitor Deposited 2022-06-29	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 2–303（302 aa） Chain B 2–303（302 aa）	Not recorded	SE1 2-[(2-{[(3s,5s,7s)-adamantan-1-yl]sulfamoyl}phenyl)sulfanyl]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；1.9 M sodium formate, 0.1 M sodium citrate, pH 5.0-5.7	Resolution 3.20 Å R-free 0.249

46 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CASP7_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–173； UniProt 24–196 Author chain C； PDBConstruct 1–173； UniProt 24–196 Author chain B； PDBConstruct 1–97； UniProt 207–303 Author chain D； PDBConstruct 1–97； UniProt 207–303

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ibf
Deposition date deposition_date	2009-07-15
Structure title title	Crystal structure of unliganded caspase-7
Keywords keywords	protein structure, Alternative splicing, Apoptosis, Cytoplasm, Hydrolase, Polymorphism, Protease, Thiol protease, Zymogen; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	23.21 Å
Radius of gyration Rg (electron density) rg_electron	21.86 Å
Forward intensity I(0) i0	48155100.00
Molecular weight molecular_weight	53579.0 kDa
Excluded volume excluded_volume	66847 Å³
Envelope volume envelope_volume	76824 Å³
Hydration-shell volume shell_volume	28271 Å³
Envelope diameter envelope_diameter	71.3 Å
Shell Rg shell_rg	29.61 Å
Envelope Rg envelope_rg	22.02 Å
Shape Rg shape_rg	21.86 Å
Total Rg total_rg	22.73 Å
Total atoms total_atoms	3760
Residues n_residues	469
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	69.6 Å
Rg (real space) rg_real	23.09 Å
Rg uncertainty (real space) rg_real_error	0.10 Å
I(0) (real space) i0_real	4.6620e+07
I(0) uncertainty (real space) i0_real_error	4.1990e+05
Rg (reciprocal space) rg_reciprocal	23.08 Å
I(0) (reciprocal space) i0_reciprocal	48160000.0000
Solution quality estimate total_estimate	0.7282
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.0 Å
Skewness Skewness skewness	0.097
Kurtosis Kurtosis kurtosis	-0.511
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	7.9400
Highest regularization parameter α highest_alpha	8768000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.950; Stabil: 0.920; Sysdev: 0.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.890

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Caspase-7
Molecular weight formula_weight	19564.6 kDa
EC 编号 ec_number	3.4.22.60
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3804

AKPDRSSFVPSLFSKKKKNVTMRSIKTTRDRVPTYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Caspase-7
Molecular weight formula_weight	11352.9 kDa
EC 编号 ec_number	3.4.22.60
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ANPRYKIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSDDPHFHEKKQIPCVVSMLTKELYFSQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3ibfA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1460 —

Domain ID domain_id	3ibfB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1470 — Caspase-like

Domain ID domain_id	3ibfC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1460 —

Domain ID domain_id	3ibfD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1470 — Caspase-like

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8. Citations (1)

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Unit-cell length a length_a	89.197 Å
Unit-cell length b length_b	89.197 Å
Unit-cell length c length_c	185.365 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2190
R_work r_work	0.2040
R_free r_free	0.2350

fit	/app/data/saxs_computation/ib/3ibf/3ibf.fit
pddf	/app/data/pr_computation/ib/3ibf/3ibf.pr.out
profile	/app/data/saxs_computation/ib/3ibf/3ibf.dat

Crystal structure of unliganded caspase-7

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

Caspase-7

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)