2hbq

Crystal structure of wildtype human caspase-1 in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)

Method: X-RAY DIFFRACTION D_max: 73.3 Å Quality: GOOD

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

Caspase-1

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 120–297 Chain B； UniProt 317–404	Fragment：P20 Subunit, residues 120-297 Fragment：P10 Subunit, residues 317-404	N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M Pipes, 200 MM LI2SO4, 25% PEG 2000 MME, 10 MM DTT, 3 MM NAN3, 2 MM MGCL2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.236

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 2HBQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BMQ CRYSTAL STRUCTURE OF THE COMPLEX OF INTERLEUKIN-1BETA CONVERTING ENZYME (ICE) WITH A PEPTIDE BASED INHIBITOR, (3S )-N-METHANESULFONYL-3-({1-[N-(2-NAPHTOYL)-L-VALYL]-L-PROLYL }AMINO)-4-OXOBUTANAMIDE Deposited 1998-07-24	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 131–297（167 aa） Chain B 317–404（88 aa）	Not recorded	MNO (3S)-N-METHANESULFONYL-3-({1-[N-(2-NAPHTOYL)-L-VALYL]-L-PROLYL}AMINO)-4-OXOBUTANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN WAS CRYSTALLIZED FROM 10-15% PEG 6000, 100MM HEPES PH 7.0	Resolution 2.50 Å R-free 0.317
1BMQ CRYSTAL STRUCTURE OF THE COMPLEX OF INTERLEUKIN-1BETA CONVERTING ENZYME (ICE) WITH A PEPTIDE BASED INHIBITOR, (3S )-N-METHANESULFONYL-3-({1-[N-(2-NAPHTOYL)-L-VALYL]-L-PROLYL }AMINO)-4-OXOBUTANAMIDE Deposited 1998-07-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 131–297（167 aa） Chain B 317–404（88 aa）	Not recorded	MNO (3S)-N-METHANESULFONYL-3-({1-[N-(2-NAPHTOYL)-L-VALYL]-L-PROLYL}AMINO)-4-OXOBUTANAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN WAS CRYSTALLIZED FROM 10-15% PEG 6000, 100MM HEPES PH 7.0	Resolution 2.50 Å R-free 0.317
1IBC CRYSTAL STRUCTURE OF INHIBITED INTERLEUKIN-1BETA CONVERTING ENZYME Deposited 1997-02-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 104–297（194 aa） Chain B 317–404（88 aa）	Mutation：D381A Mutation：D381A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；1.5 ML DROPS OF PROTEIN-INHIBITOR SOLUTION (5.0 MG/ML IN 10 MILLIMOLAR TRIS-HCL, PH 8.5, 10 MILLI-MOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (7.2% PEG-6000 (W:W), 0.10 M PIPES PH 5.8, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) AND INCUBATED AT ROOM TEMPERATURE.	Resolution 2.73 Å R-free 0.285
1ICE STRUCTURE AND MECHANISM OF INTERLEUKIN-1BETA CONVERTING ENZYME Deposited 1994-09-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 131–297（167 aa） Chain B 317–404（88 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1RWK Crystal structure of human caspase-1 in complex with 3-(2-mercapto-acetylamino)-4-oxo-pentanoic acid Deposited 2003-12-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 120–297（178 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P20 Chain B 317–404（88 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P10	Not recorded	158 3-(2-MERCAPTO-ACETYLAMINO)-4-OXO-PENTANOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；274 K；0.1M HEPES, 2M (NH4)2SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 274K	Resolution 2.30 Å R-free 0.258
1RWM Crystal structure of human caspase-1 in complex with 4-oxo-3-[2-(5-{[4-(quinoxalin-2-ylamino)-benzoylamino]-methyl}-thiophen-2-yl)-acetylamino]-pentanoic acid Deposited 2003-12-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 120–297（178 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P20 Chain B 317–404（88 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P10	Not recorded	Q2Y 4-OXO-3-[2-(5-{[4-(QUINOXALIN-2-YLAMINO)-BENZOYLAMINO]-METHYL}-THIOPHEN-2-YL)-ACETYLAMINO]-PENTANOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；278 K；0.1M PIPES, 200mM Li2SO4, 25% PEG2K MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.70 Å R-free 0.254
1RWN Crystal structure of human caspase-1 in complex with 3-{2-ethyl-6-[4-(quinoxalin-2-ylamino)-benzoylamino]-hexanoylamino}-4-oxo-butyric acid Deposited 2003-12-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 120–297（178 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P20 Chain B 317–404（88 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P10	Not recorded	4QB 3-{2-ETHYL-6-[4-(QUINOXALIN-2-YLAMINO)-BENZOYLAMINO]-HEXANOYLAMINO}-4-OXO-BUTYRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；278 K；0.1M PIPES, 175mM (NH4)2SO4, 25% PEG2K MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.00 Å R-free 0.236
1RWO Crystal structure of human caspase-1 in complex with 4-oxo-3-{6-[4-(quinoxalin-2-ylamino)-benzoylamino]-2-thiophen-2-yl-hexanoylamino}-pentanoic acid Deposited 2003-12-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 120–297（178 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P20 Chain B 317–404（88 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P10	Not recorded	BTH 4-OXO-3-{6-[4-(QUINOXALIN-2-YLAMINO)-BENZOYLAMINO]-2-THIOPHEN-2-YL-HEXANOYLAMINO}-PENTANOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；278 K；0.1M PIPES, 200mM Li2SO4, 25% PEG2K MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.10 Å R-free 0.242
1RWP Crystal structure of human caspase-1 in complex with 3-{6-[(8-hydroxy-quinoline-2-carbonyl)-amino]-2-thiophen-2-yl-hexanoylamino}-4-oxo-butyric acid Deposited 2003-12-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 120–297（178 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P20 Chain B 317–404（88 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P10	Not recorded	HQC 3-{6-[(8-HYDROXY-QUINOLINE-2-CARBONYL)-AMINO]-2-THIOPHEN-2-YL-HEXANOYLAMINO}-4-OXO-BUTYRI ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；278 K；0.1M PIPES, 175mM (NH4)2SO4, 25% PEG2K MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.20 Å R-free 0.245
1RWV Crystal structure of human caspase-1 in complex with 5-[5-(1-carboxymethyl-2-oxo-propylcarbamoyl)-5-phenyl-pentylsulfamoyl]-2-hydroxy-benzoic acid Deposited 2003-12-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 120–297（178 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P20 Chain B 317–404（88 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P10	Not recorded	5PH 5-[5-(1-CARBOXYMETHYL-2-OXO-PROPYLCARBAMOYL)-5-PHENYL-PENTYLSULFAMOYL]-2-HYDROXY-BENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；278 K；0.1M PIPES, 14% PEG 6000, 10mM DTT, 3mM NaN3, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.10 Å R-free 0.238
1RWW Crystal structure of human caspase-1 in complex with 4-oxo-3-[(6-{[4-(quinoxalin-2-ylamino)-benzoylamino]-methyl}-pyridine-3-carbonyl)-amino]-butyric acid Deposited 2003-12-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 120–297（178 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P20 Chain B 317–404（88 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P10	Not recorded	OQB 4-OXO-3-[(6-{[4-(QUINOXALIN-2-YLAMINO)-BENZOYLAMINO]-METHYL}-PYRIDINE-3-CARBONYL)-AMINO]-BUTYRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；278 K；0.1M PIPES, 192mM (NH4)2SO4, 25% PEG 2000 MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.80 Å R-free 0.246
1RWX Crystal structure of human caspase-1 in complex with 4-oxo-3-{6-[4-(quinoxalin-2-yloxy)-benzoylamino]-2-thiophen-2-yl-hexanoylamino}-butyric acid Deposited 2003-12-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 120–297（178 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P20 Chain B 317–404（88 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P10	Not recorded	YBH 4-OXO-3-{6-[4-(QUINOXALIN-2-YLOXY)-BENZOYLAMINO]-2-THIOPHEN-2-YL-HEXANOYLAMINO}-BUTYRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；278 K；0.1M PIPES, 88mM (NH4)2SO4, 25% PEG 2000 MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 1.85 Å R-free 0.242
1SC1 Crystal structure of an active-site ligand-free form of the human caspase-1 C285A mutant Deposited 2004-02-11	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 120–297（178 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P20 Chain B 317–404（88 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P10	Mutation：C285A	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；278 K；0.1 M HEPES, 2 M (NH4)2SO4, 25 mM DTT. 0.01% Triton-X was added to the drop to prevent the crystals from attaching themselves to the cover slips., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.60 Å R-free 0.273
1SC3 Crystal structure of the human caspase-1 C285A mutant in complex with malonate Deposited 2004-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 120–297（178 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P20 Chain B 317–404（88 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P10	Mutation：C285A	MLI MALONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；274 K；2 M sodium malonate, VAPOR DIFFUSION, HANGING DROP, temperature 274K	Resolution 1.80 Å R-free 0.238
1SC4 Crystal structure of the human caspase-1 C285A mutant after removal of malonate Deposited 2004-02-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 120–297（178 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P20 Chain B 317–404（88 aa） Fragment：INTERLEUKIN-1 BETA CONVERTASE P10	Mutation：C285A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；274 K；2 M sodium malonate, VAPOR DIFFUSION, HANGING DROP, temperature 274K. Malonate-bound enzyme crystals were transferred into mother liquor composed of 0.1 M PIPES pH 6, 88 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3 and 2 mM MgCl2, and soaked for 2 days to remove malonate.	Resolution 2.10 Å R-free 0.258
2FQQ Crystal structure of human caspase-1 (Cys285->Ala, Cys362->Ala, Cys364->Ala, Cys397->Ala) in complex with 1-methyl-3-trifluoromethyl-1H-thieno[2,3-c]pyrazole-5-carboxylic acid (2-mercapto-ethyl)-amide Deposited 2006-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 120–297（178 aa） Fragment：p20 subunit, residues 120-297 Chain B 317–404（88 aa） Fragment：p10 subunit, residues 317-404	Mutation：C285A Mutation：C362A, C364A, C397A	F1G 1-METHYL-3-TRIFLUOROMETHYL-1H-THIENO[2,3-C]PYRAZOLE-5-CARBOXYLIC ACID (2-MERCAPTO-ETHYL)-AMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；10 mM HEPES, 16.5% PEG 3350, 250 mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.30 Å R-free 0.280
2H48 Crystal structure of human caspase-1 (Cys362->Ala, Cys364->Ala, Cys397->Ala) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK) Deposited 2006-05-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 120–297（178 aa） Fragment：large subunit, residues, 120-297 Chain B 317–404（88 aa） Fragment：small subunit, residues 317-404	Mutation：C362A, C364A, C397A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1M Pipes pH 6.0, 200 mM ammonium sulfate, 25% PEG 2000 MME, 10 mM DTT, 2 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.272
2H4W Crystal structure of human caspase-1 (Glu390->Asp) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK) Deposited 2006-05-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 120–297（178 aa） Fragment：p20 subunit, residues 120-297 Chain B 317–404（88 aa） Fragment：p10 subunit, residues 317-404	Mutation：E390D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M PIPES, 200 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, 2 mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.247
2H4Y Crystal structure of human caspase-1 (Arg286->Lys) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK) Deposited 2006-05-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 120–297（178 aa） Fragment：p20 subunit, residues 120-297 Chain B 317–404（88 aa） Fragment：p10 subunit, residues 317-404	Mutation：R286K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M PIPES, 200 mM Li2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, 2 mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.235
2H51 Crystal structure of human caspase-1 (Glu390->Asp and Arg286->Lys) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK) Deposited 2006-05-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 120–297（178 aa） Fragment：p20 subunit, residues 120-297 Chain B 317–404（88 aa） Fragment：p10 subunit, residues 317-404	Mutation：R286K Mutation：E390D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M PIPES, 200 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, 2 mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.236
2H54 Crystal structure of human caspase-1 (Thr388->Ala) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK) Deposited 2006-05-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 120–297（178 aa） Fragment：p20 subunit, residues 120-297 Chain B 317–404（88 aa） Fragment：p10 subunit, residues 317-404	Mutation：T388A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M PIPES, 200 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, 2 mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.246
2HBR Crystal structure of human caspase-1 (Arg286->Ala) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK) Deposited 2006-06-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 120–297（178 aa） Fragment：P20 Subunit, residues 120-297 Chain B 317–404（88 aa） Fragment：P10 Subunit, residues 317-404	Mutation：R286A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, 2 M (NH4)2SO4, 25 MM DTT, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.270
2HBY Crystal structure of human caspase-1 (Glu390->Ala) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK) Deposited 2006-06-14	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 120–297（178 aa） Fragment：P20 Subunit, Residues 120-297 Chain B 317–404（88 aa） Fragment：P10 Subunit, Residues 317-404	Mutation：E390A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M Pipes, 350 MM LI2SO4, 20% PEG 2000 MME, 10 MM DTT, 3 MM NAN3, 2 MM MGCL2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.258
2HBZ Crystal structure of human caspase-1 (Arg286->Ala, Glu390->Ala) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK) Deposited 2006-06-14	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 120–297（178 aa） Fragment：P20 Subunit, Residues 120-297 Chain B 317–404（88 aa） Fragment：P10 Subunit, Residues 317-404	Mutation：R286A Mutation：E390A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M Pipes, 100 MM LI2SO4, 25% PEG 2000 MME, 10 MM DTT, 3 MM NAN3, 2 MM MGCL2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.249
3D6F Crystal structure of human caspase-1 with a naturally-occurring Arg240->Gln substitution in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK) Deposited 2008-05-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 120–297（178 aa） Fragment：Caspase-1 subunit p20 Chain B 317–404（88 aa） Fragment：Caspase-1 subunit p10	Mutation：R240Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；Crystals obtained by hanging-drop vapor diffusion at 4 C (277K) against a reservoir of 0.1 M PIPES pH 6.0, 75-175 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, and 2 mM MgCl2. All crystals cryoprotected in mother liquors supplemented with 20% (v/v) glycerol for 30-90 sec and immersion in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP	Resolution 1.90 Å R-free 0.240
3D6H Crystal structure of human caspase-1 with a naturally-occurring Asn263->Ser substitution in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK) Deposited 2008-05-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 120–297（178 aa） Fragment：Caspase-1 subunit p20 Chain B 317–404（88 aa） Fragment：Caspase-1 subunit p10	Mutation：N263S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；Crystals obtained by hanging-drop vapor diffusion at 4 C (277K) against a reservoir of 0.1 M PIPES pH 6.0, 75-175 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, and 2 mM MgCl2. All crystals cryoprotected in mother liquors supplemented with 20% (v/v) glycerol for 30-90 sec and immersion in liquid nitrogen. , VAPOR DIFFUSION, HANGING DROP	Resolution 2.00 Å R-free 0.237
3D6M Crystal structure of human caspase-1 with a naturally-occurring Lys319->Arg substitution in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK) Deposited 2008-05-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 120–297（178 aa） Fragment：CASP1 p20 Chain B 317–404（88 aa） Fragment：CASP1 p10	Mutation：K319R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；Crystals obtained by hanging-drop vapor diffusion at 4 C (277K) against a reservoir of 0.1 M PIPES pH 6.0, 75-175 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, and 2 mM MgCl2. All crystals cryoprotected in mother liquors supplemented with 20% (v/v) glycerol for 30-90 sec and immersion in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP	Resolution 1.80 Å R-free 0.247
3E4C Procaspase-1 zymogen domain crystal structure Deposited 2008-08-11	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 104–404（301 aa） Fragment：procaspase-1 zymogen domain (UNP residues 104-404) Chain B 104–404（301 aa） Fragment：procaspase-1 zymogen domain (UNP residues 104-404)	Mutation：C285A Mutation：C285A	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；277 K；0.2 M MgCl2 20% PEG 3350, pH 7.5, EVAPORATION, temperature 277K	Resolution 2.05 Å R-free 0.263
3NS7 Succinic Acid Amides as P2-P3 Replacements for Inhibitors of Interleukin-1beta Converting Enzyme (ICE or Caspase 1) Deposited 2010-07-01	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 136–297（162 aa） Fragment：UNP residues 136-297 Chain B 317–404（88 aa） Fragment：UNP residues 317-404	Not recorded	3NS (3S)-4-hydroxy-3-{[(2S)-4-{[2-(2-methyl-1H-benzimidazol-1-yl)ethyl]amino}-2-(1-methylethyl)-4-oxobutanoyl]amino}butanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；276 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 276K	Resolution 2.60 Å
3NS7 Succinic Acid Amides as P2-P3 Replacements for Inhibitors of Interleukin-1beta Converting Enzyme (ICE or Caspase 1) Deposited 2010-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 136–297（162 aa） Fragment：UNP residues 136-297 Chain B 317–404（88 aa） Fragment：UNP residues 317-404	Not recorded	3NS (3S)-4-hydroxy-3-{[(2S)-4-{[2-(2-methyl-1H-benzimidazol-1-yl)ethyl]amino}-2-(1-methylethyl)-4-oxobutanoyl]amino}butanoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；276 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 276K	Resolution 2.60 Å
5FNA Cryo-EM reconstruction of caspase-1 CARD Deposited 2015-11-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 2–86（85 aa） Fragment：CARD DOMAIN Chain B 2–86（85 aa） Fragment：CARD DOMAIN Chain C 2–86（85 aa） Fragment：CARD DOMAIN Chain D 2–86（85 aa） Fragment：CARD DOMAIN Chain E 2–86（85 aa） Fragment：CARD DOMAIN Chain F 2–86（85 aa） Fragment：CARD DOMAIN Chain G 2–86（85 aa） Fragment：CARD DOMAIN Chain H 2–86（85 aa） Fragment：CARD DOMAIN	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20 MM SODIUM HEPES, 150 MM NACL, 2 MM DTT；pH 8；20 MM SODIUM HEPES, 150 MM NACL, 2 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 4.80 Å
5MMV Crystal structure of human Caspase-1 with 2-((2-naphthoyl)-L-valyl)-4-hydroxy-N-((3S)-2-hydroxy-5-oxotetrahydrofuran-3-yl)-2-azabicyclo[2.2.2]octane-3-carboxamide (Compound 1) Deposited 2016-12-12	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 120–297（178 aa） Chain B 317–404（88 aa）	Not recorded	WE0 (3~{S})-3-[[(3~{S})-2-[(2~{S})-3-methyl-2-(naphthalen-2-ylcarbonylamino)butanoyl]-4-oxidanyl-2-azabicyclo[2.2.2]octan-3-yl]carbonylamino]-4-oxidanyl-butanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.1 M HEPES (pH 7.4), 2 M (NH4)2SO4, and 25 mM DTT	Resolution 2.15 Å R-free 0.249
5MTK Crystal structure of human Caspase-1 with (3S,6S,10aS)-N-((2S,3S)-2-hydroxy-5-oxotetrahydrofuran-3-yl)-6-(isoquinoline-1-carboxamido)-5-oxodecahydropyrrolo[1,2-a]azocine-3-carboxamide (PGE-3935199) Deposited 2017-01-09	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 120–297（178 aa） Chain B 317–404（88 aa）	Not recorded	N7N (3~{S})-3-[[(3~{S},6~{S},10~{a}~{S})-6-(isoquinolin-1-ylcarbonylamino)-5-oxidanylidene-2,3,6,7,8,9,10,10~{a}-octahydro-1~{H}-pyrrolo[1,2-a]azocin-3-yl]carbonylamino]-4-oxidanyl-butanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES (pH 7.4), 2 M (NH4)2SO4 and 25 mM DTT	Resolution 2.53 Å R-free 0.299
6BZ9 Crystal structure of human caspase-1 in complex with Ac-FLTD-CMK Deposited 2017-12-22	Different construct 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 120–297（178 aa） Fragment：UNP residues 120-297 Chain B 317–404（88 aa） Fragment：UNP residues 317-404	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M sodium formate, 20% w/v PEG3350	Resolution 1.80 Å R-free 0.210
6F6R Crystal structure of human Caspase-1 with N-{3-[1-((S)-2-Hydroxy-5-oxo-tetrahydro-furan-3-ylcarbamoyl)-ethyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydro-pyrimidin-5-yl}-4-(quinoxalin-2-ylamino)-benzamide Deposited 2017-12-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 118–297（180 aa） Chain B 317–404（88 aa）	Not recorded	CVE (3~{S})-3-[[(2~{R})-2-[3-methyl-2,6-bis(oxidanylidene)-5-[[4-(quinoxalin-2-ylamino)phenyl]carbonylamino]pyrimidin-1-yl]propanoyl]amino]-4-oxidanyl-butanoic acid × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES (pH7.4), 2 M (NH4)2SO4 and 25 mM DTT	Resolution 1.80 Å R-free 0.205
6F6R Crystal structure of human Caspase-1 with N-{3-[1-((S)-2-Hydroxy-5-oxo-tetrahydro-furan-3-ylcarbamoyl)-ethyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydro-pyrimidin-5-yl}-4-(quinoxalin-2-ylamino)-benzamide Deposited 2017-12-06	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 A 118–297（180 aa） Chain B 317–404（88 aa）	Not recorded	CVE (3~{S})-3-[[(2~{R})-2-[3-methyl-2,6-bis(oxidanylidene)-5-[[4-(quinoxalin-2-ylamino)phenyl]carbonylamino]pyrimidin-1-yl]propanoyl]amino]-4-oxidanyl-butanoic acid × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES (pH7.4), 2 M (NH4)2SO4 and 25 mM DTT	Resolution 1.80 Å R-free 0.205
6KN0 caspase-1 P20/P10 C285A in complex with human GSDMD-C domain Deposited 2019-08-02	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 131–297（167 aa） Chain B 317–404（88 aa）	Mutation：C285A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；150 mM KBr, 30% (w/v) polyethylene glycol mono-methyester 2000	Resolution 2.79 Å R-free 0.300
6KN0 caspase-1 P20/P10 C285A in complex with human GSDMD-C domain Deposited 2019-08-02	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 131–297（167 aa） Chain D 317–404（88 aa）	Mutation：C285A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；150 mM KBr, 30% (w/v) polyethylene glycol mono-methyester 2000	Resolution 2.79 Å R-free 0.300
6PZP Crystal structure of caspase-1 in complex with VX-765 Deposited 2019-08-01	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 120–297（178 aa） Chain B 317–404（88 aa）	Not recorded	P7S N-(4-amino-3-chlorobenzene-1-carbonyl)-3-methyl-L-valyl-N-[(2S)-1-carboxy-3-oxopropan-2-yl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M sodium formate, 20% w/v PEG3350	Resolution 1.94 Å R-free 0.208
6VIE Structure of caspase-1 in complex with gasdermin D Deposited 2020-01-13	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 120–303（184 aa） Fragment：residues 120-316 Chain B 317–404（88 aa） Fragment：residues 317-404	Mutation：C285A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M Ammonium citrate tribasic pH 7.0, 20% PEG3350	Resolution 3.40 Å R-free 0.314
7KEU Cryo-EM structure of the Caspase-1-CARD:ASC-CARD octamer Deposited 2020-10-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 2–86（85 aa） Fragment：UNP residues 2-86 Chain F 2–86（85 aa） Fragment：UNP residues 2-86 Chain G 2–86（85 aa） Fragment：UNP residues 2-86 Chain H 2–86（85 aa） Fragment：UNP residues 2-86	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8SV1 Caspase-1 complex with interleukin-18 Deposited 2023-05-15	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 150–297（148 aa） Fragment：subunit P20 (UNP residues 120-297) Chain B 317–404（88 aa） Fragment：subunit P10 (UNP residues 317-404) Chain a 150–297（148 aa） Fragment：subunit P20 (UNP residues 120-297) Chain b 317–404（88 aa） Fragment：subunit P10 (UNP residues 317-404)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8WRA The Crystal Structure of CASP1 from Biortus Deposited 2023-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–404（285 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.15M Na formate, 14% PEG3350	Resolution 1.45 Å R-free 0.213
8WRA The Crystal Structure of CASP1 from Biortus Deposited 2023-10-13	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 A 120–404（285 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.15M Na formate, 14% PEG3350	Resolution 1.45 Å R-free 0.213
9WZ6 Full-length Caspase-1-CARD filament Deposited 2025-09-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–404（404 aa） Chain B 1–404（404 aa） Chain C 1–404（404 aa） Chain D 1–404（404 aa） Chain E 1–404（404 aa） Chain F 1–404（404 aa） Chain G 1–404（404 aa） Chain H 1–404（404 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.66 Å
9WZI Full-length Caspase-1-CARD filament Deposited 2025-09-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–404（404 aa） Chain B 1–404（404 aa） Chain C 1–404（404 aa） Chain D 1–404（404 aa） Chain E 1–404（404 aa） Chain F 1–404（404 aa） Chain G 1–404（404 aa） Chain H 1–404（404 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å

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

View Construct and Data Evidence

UniProt name	CASP1_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–178； UniProt 120–297 Author chain B； PDBConstruct 1–88； UniProt 317–404

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	2hbq
Deposition date deposition_date	2006-06-14
Structure title title	Crystal structure of wildtype human caspase-1 in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)
Keywords keywords	active-site inhibitor, allosteric circuit, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	19.58 Å
Radius of gyration Rg (electron density) rg_electron	18.44 Å
Forward intensity I(0) i0	15743900.00
Molecular weight molecular_weight	29335.0 kDa
Excluded volume excluded_volume	36538 Å³
Envelope volume envelope_volume	43317 Å³
Hydration-shell volume shell_volume	19421 Å³
Envelope diameter envelope_diameter	72.9 Å
Shell Rg shell_rg	25.28 Å
Envelope Rg envelope_rg	19.23 Å
Shape Rg shape_rg	18.44 Å
Total Rg total_rg	19.45 Å
Total atoms total_atoms	2053
Residues n_residues	259
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	73.3 Å
Rg (real space) rg_real	19.49 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.5740e+07
I(0) uncertainty (real space) i0_real_error	2.2770e+05
Rg (reciprocal space) rg_reciprocal	19.51 Å
I(0) (reciprocal space) i0_reciprocal	15740000.0000
Solution quality estimate total_estimate	0.8192
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.256
Kurtosis Kurtosis kurtosis	-0.211
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3271000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.574; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Caspase-1
Molecular weight formula_weight	19869.8 kDa
EC 编号 ec_number	3.4.22.36
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2294

NPAMPTSSGSEGNVKLCSLEEAQRIWKQKSAEIYPIMDKSSRTRLALIICNEEFDSIPRRTGAEVDITGMTMLLQNLGYSVDVKKNLTASDMTTELEAFAHRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQLNAIFNMLNTKNCPSLKDKPKVIIIQACRGDSPGVVWFKD

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-1
Molecular weight formula_weight	10258.8 kDa
EC 编号 ec_number	3.4.22.36
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AIKKAHIEKDFIAFCSSTPDNVSWRHPTMGSVFIGRLIEHMQEYACSCDVEEIFRKVRFSFEQPDGRAQMPTTERVTLTRCFYLFPGH

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 polymer

Description description	N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide
Molecular weight formula_weight	471.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

XVADX

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	229

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2hbqA00
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	2hbqB00
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	63.301 Å
Unit-cell length b length_b	63.301 Å
Unit-cell length c length_c	161.681 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2100
R_work r_work	0.2080
R_free r_free	0.2360

fit	/app/data/saxs_computation/hb/2hbq/2hbq.fit
pddf	/app/data/pr_computation/hb/2hbq/2hbq.pr.out
profile	/app/data/saxs_computation/hb/2hbq/2hbq.dat

Crystal structure of wildtype human caspase-1 in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)

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

Caspase-1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)