6px9

Crystal structure of procaspase-8 in complex with covalent small molecule inhibitor 63-R

Method: X-RAY DIFFRACTION D_max: 126.0 Å Quality: GOOD

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

Caspase-8

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 276–538 Chain B； UniProt 276–538	Fragment：UNP residues 276-538 Mutation：D374A, D384A, C409S, C433S	63R N-{(3R)-1-[4-(morpholin-4-yl)benzene-1-carbonyl]piperidin-3-yl}-N-phenylacetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M imidazole, pH 8.0, 1.0 M sodium citrate	Resolution 2.88 Å R-free 0.366
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 276–538 Chain D； UniProt 276–538	Fragment：UNP residues 276-538 Mutation：D374A, D384A, C409S, C433S	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M imidazole, pH 8.0, 1.0 M sodium citrate	Resolution 2.88 Å R-free 0.366
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 276–538 Chain F； UniProt 276–538	Fragment：UNP residues 276-538 Mutation：D374A, D384A, C409S, C433S	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M imidazole, pH 8.0, 1.0 M sodium citrate	Resolution 2.88 Å R-free 0.366

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 6PX9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F9E CASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO Deposited 2000-07-10	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 222–374（153 aa） Chain B 390–478（89 aa） Chain C 222–374（153 aa） Chain D 390–478（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1-propanol, sodium citrate, MES , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K, temperature 277K	Resolution 2.90 Å R-free 0.289
1F9E CASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO Deposited 2000-07-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 222–374（153 aa） Chain F 390–478（89 aa） Chain G 222–374（153 aa） Chain H 390–478（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1-propanol, sodium citrate, MES , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K, temperature 277K	Resolution 2.90 Å R-free 0.289
1F9E CASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO Deposited 2000-07-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 222–374（153 aa） Chain J 390–478（89 aa） Chain K 222–374（153 aa） Chain L 390–478（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1-propanol, sodium citrate, MES , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K, temperature 277K	Resolution 2.90 Å R-free 0.289
1I4E CRYSTAL STRUCTURE OF THE CASPASE-8/P35 COMPLEX Deposited 2001-02-20	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 B 222–479（258 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 3.00 Å R-free 0.296
1I4E CRYSTAL STRUCTURE OF THE CASPASE-8/P35 COMPLEX Deposited 2001-02-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 222–479（258 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 3.00 Å R-free 0.296
1QDU CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TRIPEPTIDE KETONE INHIBITOR ZEVD-DCBMK Deposited 1999-07-10	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 222–374（153 aa） Chain B 390–477（88 aa） Chain C 222–374（153 aa） Chain D 390–477（88 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；300mM ammonium phosphate, 27% (w/v) isopropanol, 100mM sodium phosphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.302
1QDU CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TRIPEPTIDE KETONE INHIBITOR ZEVD-DCBMK Deposited 1999-07-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 222–374（153 aa） Chain F 390–477（88 aa） Chain G 222–374（153 aa） Chain H 390–477（88 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；300mM ammonium phosphate, 27% (w/v) isopropanol, 100mM sodium phosphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.302
1QDU CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TRIPEPTIDE KETONE INHIBITOR ZEVD-DCBMK Deposited 1999-07-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 222–374（153 aa） Chain J 390–477（88 aa） Chain K 222–374（153 aa） Chain L 390–477（88 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；300mM ammonium phosphate, 27% (w/v) isopropanol, 100mM sodium phosphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.302
1QTN CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TETRAPEPTIDE INHIBITOR ACE-IETD-ALDEHYDE Deposited 1999-06-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 223–374（152 aa） Fragment：P18 FRAGMENT Chain B 390–479（90 aa） Fragment：P11 FRAGMENT	Not recorded	DTD DITHIANE DIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；282 K；3 MICROLITERS PROTEIN (8.4 MG/ ML IN 20 MM TRISHCL, 100MM DTT AT PH 8.0) MIXED WITH 3 MICROLITERS WELL BUFFER (1.4 SODIUM CITRATE, 0.1M HEPES, AT PH 8.0) AT 4 DEG. C, VAPOR DIFFUSION, SITTING DROP, temperature 282K	Resolution 1.20 Å R-free 0.188
2C2Z Crystal structure of caspase-8 in complex with aza-peptide Michael acceptor inhibitor Deposited 2005-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 218–374（157 aa） Fragment：ALPHA SUB-UNIT, RESIDUES 218-374 Chain B 376–479（104 aa） Fragment：BETA-SUBUNIT, RESIDUES 376-479	Not recorded	DTD DITHIANE DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；1.4M SODIUM CITRATE, 100MM HEPES PH 8.0	Resolution 1.95 Å R-free 0.187
2FUN alternative p35-caspase-8 complex Deposited 2006-01-27	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 B 222–479（258 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；VAPOR DIFFUSION, HANGING DROP, pH 7, temperature 295K	Resolution 3.00 Å R-free 0.260
2FUN alternative p35-caspase-8 complex Deposited 2006-01-27	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 D 222–479（258 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；VAPOR DIFFUSION, HANGING DROP, pH 7, temperature 295K	Resolution 3.00 Å R-free 0.260
2K7Z Solution Structure of the Catalytic Domain of Procaspase-8 Deposited 2008-08-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 217–479（263 aa） Fragment：UNP residues 213-479	Mutation：C360A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；305 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] procaspase8, 10 mM DTT, 100 mM sodium chloride, 20 mM [U-2H] TRIS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N; 80% 2H] procaspase8, 10 mM DTT, 100 mM sodium chloride, 20 mM [U-2H] TRIS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2Y1L Caspase-8 in Complex with DARPin-8.4 Deposited 2010-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: octameric	Chain A 217–374（158 aa） Fragment：P18 SUBUNIT, RESIDUES 218-374 Chain B 376–479（104 aa） Fragment：P10 SUBUNIT, RESIDUES 376-479 Chain C 217–374（158 aa） Fragment：P18 SUBUNIT, RESIDUES 218-374 Chain D 376–479（104 aa） Fragment：P10 SUBUNIT, RESIDUES 376-479	Not recorded	SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；100 MM CITRIC ACID PH 4.9 (RT), 200 MM LI2SO4, 22.5% PEG 4K.	Resolution 1.80 Å R-free 0.218
3H11 Zymogen caspase-8:c-FLIPL protease domain complex Deposited 2009-04-10	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 217–479（263 aa）	Mutation：D359A, D369A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；293 K；0.9 M sodium dihydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.1 M N-cyclohexyl-3-aminopropanesulfonic acid (CAPS), 0.2 M lithium sulfate, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.250
3KJN Caspase 8 bound to a covalent inhibitor Deposited 2009-11-03	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 211–374（164 aa） Fragment：residues 211-374 Chain B 385–479（95 aa） Fragment：residues 385-479	Not recorded	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 B93 (3S)-3-({[(5S)-2-{2-[(1H-benzimidazol-5-ylcarbonyl)amino]ethyl}-7-(cyclohexylmethyl)-1,3-dioxo-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazin-5-yl]carbonyl}amino)-4-oxopentanoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；2 microliters of 100 mM inhibitor stock in DMSO was added to 100 microliters of 8.4 mg/mL protein in 20 mM Tris, 100 mM DTT, pH 8.0. Protein solution was mixed with an equal volume of well solution (1.0-1.1 M Citrate, 50 mM HEPES or PIPES pH 6.5, 25 mM DTT), VAPOR DIFFUSION, temperature 277K	Resolution 1.80 Å R-free 0.202
3KJQ Caspase 8 with covalent inhibitor Deposited 2009-11-03	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 211–374（164 aa） Chain B 385–479（95 aa）	Not recorded	B94 (3S)-3-({[(5S,8R)-2-(3-carboxypropyl)-8-(2-{[(4-chlorophenyl)acetyl]amino}ethyl)-1,3-dioxo-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazin-5-yl]carbonyl}amino)-4-oxopentanoic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；277 K；2 microliters of 100 mM inhibitor stock in DMSO was added to 100 microliters of 8.4 mg/mL protein in 20 mM Tris, 100 mM DTT, pH 8.0. Protein solution was mixed with an equal volume of well solution (1.0-1.1 M Citrate, 50 mM HEPES or PIPES pH 6.5, 25 mM DTT), VAPOR DIFFUSION, temperature 277K	Resolution 1.80 Å R-free 0.207
4JJ7 Caspase-3 specific unnatural amino acid-based peptides Deposited 2013-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 217–479（263 aa）	Not recorded	DTD DITHIANE DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；1 M Sodium citrate, 0.1M HEPES pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.18 Å R-free 0.157
4PRZ Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06	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 217–479（263 aa） Fragment：UNP RESIDUES 217-479	Not recorded	DTD DITHIANE DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；1.0 M sodium citrate, 0.1 M HEPES, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.12 Å R-free 0.218
4PS1 Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06	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 217–479（263 aa） Fragment：UNP RESIDUES 217-479	Not recorded	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.73 Å R-free 0.185
4PS1 Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06	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 217–479（263 aa） Fragment：UNP RESIDUES 217-479	Not recorded	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.73 Å R-free 0.185
4PS1 Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 217–479（263 aa） Fragment：UNP RESIDUES 217-479	Not recorded	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.73 Å R-free 0.185
4PS1 Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 217–479（263 aa） Fragment：UNP RESIDUES 217-479	Not recorded	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.73 Å R-free 0.185
4ZBW Crystal structure of death effector domain of Caspase8 in Homo Sapiens Deposited 2015-04-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 61–247（187 aa） Chain B 61–247（187 aa）	Mutation：F122A, I128D Mutation：F122A, I128D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；0.2M sodium chloride, 25% PEG3350	Resolution 2.20 Å R-free 0.251
5H31 Structural basis for dimerization of the death effector domains of Caspase-8 Deposited 2016-10-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–188（188 aa） Fragment：UNP residues 1-188 Chain B 1–188（188 aa） Fragment：UNP residues 1-188	Mutation：F122A Mutation：F122A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；100 mM sodium chloride, 100 mM Tris, 21% PEG3350, 10 mM Sarcosine,	Resolution 3.17 Å R-free 0.268
5H31 Structural basis for dimerization of the death effector domains of Caspase-8 Deposited 2016-10-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–188（188 aa） Fragment：UNP residues 1-188 Chain D 1–188（188 aa） Fragment：UNP residues 1-188	Mutation：F122A Mutation：F122A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；100 mM sodium chloride, 100 mM Tris, 21% PEG3350, 10 mM Sarcosine,	Resolution 3.17 Å R-free 0.268
5H33 Structural basis for dimerization of the death effector domains of Caspase-8 Deposited 2016-10-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–188（188 aa） Chain B 1–188（188 aa）	Mutation：F122A Mutation：F122A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；50mM sodium chloride, 100mM Tris pH 8.5, 22.5% PEG3350	Resolution 3.60 Å R-free 0.313
5JQE Crystal structure of caspase8 tDED Deposited 2016-05-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–186（186 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；293 K；0.1M MMT buffer, pH 8.0, 25% PEG 1500	Resolution 3.16 Å R-free 0.274
5L08 Cryo-EM structure of Casp-8 tDED filament Deposited 2016-07-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric	Chain A 60–243（184 aa） Chain B 60–243（184 aa） Chain C 60–243（184 aa） Chain D 60–243（184 aa） Chain E 60–243（184 aa） Chain F 60–243（184 aa） Chain G 60–243（184 aa） Chain H 60–243（184 aa） Chain I 60–243（184 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
6AGW Pro-domain of Caspase-8 Deposited 2018-08-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–180（180 aa） Fragment：UNP residues 1-180	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；(NH4)2SO4, Cacodylate, NaCl	Resolution 2.09 Å R-free 0.269
6X8H Caspase-8 in complex with AOMK inhibitor, Ac-DW3-KE, forms tetrahedral adduct Deposited 2020-06-01	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 276–443（168 aa） Fragment：p18 (UNP residues 276-443) Chain B 444–538（95 aa） Fragment：p10 (UNP residues 444-538)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；295 K；1:1 protein : 0.10 M HEPES, 1.0 M sodium citrate	Resolution 1.48 Å R-free 0.167
7LVM CASP8 isoform B DED domain Deposited 2021-02-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–188（187 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；100mM Hepes pH 7.5, 20% Ethylene Glycol, 18% PEG 3350, 200mM Sodium Chloride	Resolution 1.47 Å R-free 0.233
8YBX Structure of the FADD/Caspase-8/cFLIP death effector domain assembly Deposited 2024-02-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–479（479 aa） Chain B 1–479（479 aa） Chain C 1–479（479 aa）	Mutation：F122G/L123G, C360A, D374A, D384A Mutation：F122G/L123G, C360A, D374A, D384A Mutation：F122G/L123G, C360A, D374A, D384A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.68 Å
8YD7 Structure of FADD/Caspase-8/cFLIP death effector domain assembly Deposited 2024-02-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–185（185 aa） Chain B 1–185（185 aa） Chain C 1–185（185 aa） Chain D 1–185（185 aa） Chain E 1–185（185 aa）	Mutation：F122G,L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G,L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G,L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G,L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G,L123G Non-standard monomer：Yes (specific site not provided by mmCIF)	SE SELENIUM ATOM × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；HEPES, TBG, PEG8000, TCEP, sodium chloride	Resolution 3.32 Å R-free 0.231
8YD8 Structure of FADD/Caspase-8/cFLIP death effector domain assembly Deposited 2024-02-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–185（185 aa） Chain B 1–185（185 aa） Chain C 1–185（185 aa） Chain D 1–185（185 aa） Chain E 1–185（185 aa）	Mutation：F122G, L123G Mutation：F122G, L123G Mutation：F122G, L123G Mutation：F122G, L123G Mutation：F122G, L123G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；HEPES, PEG 8000, TBG, TCEP, sodium chloride	Resolution 3.11 Å R-free 0.241
8YM4 Structure of Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–185（185 aa） Chain B 1–185（185 aa） Chain C 1–185（185 aa） Chain D 1–185（185 aa）	Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF)	SE SELENIUM ATOM × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M MES pH 6.5, 0.08 M sodium chloride, 0.2 M Potassium Thiocyanate, 10 % PEG 4000, 0.01 M TCEP	Resolution 2.34 Å R-free 0.253
8YM5 Structure of Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–185（185 aa） Chain B 1–185（185 aa） Chain C 1–185（185 aa） Chain D 1–185（185 aa）	Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M MES pH 6.5, 0.08 M sodium chloride, 0.2 M Potassium Thiocyanate, 10 % PEG 4000, 0.01 M TCEP	Resolution 2.09 Å R-free 0.231
8YM6 Structure of Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 1–185（185 aa） Chain B 1–185（185 aa） Chain C 1–185（185 aa） Chain D 1–185（185 aa）	Mutation：F122G, L123G Mutation：F122G, L123G Mutation：F122G, L123G Mutation：F122G, L123G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M HEPES pH 7.5, 0.2 M Lithium chloride, 20 % PEG 400, 0.1 M TBG pH 9.0	Resolution 3.30 Å R-free 0.264
8YNI Structure of the FADD/Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: 11-meric	Chain A 1–479（479 aa） Chain B 1–479（479 aa） Chain C 1–479（479 aa）	Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.66 Å
8YNK Structure of the Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-11	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 A 1–479（479 aa） Chain B 1–479（479 aa） Chain C 1–479（479 aa）	Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
8YNL Structure of the Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–479（479 aa） Chain B 1–479（479 aa） Chain C 1–479（479 aa）	Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.55 Å
8YNM Structure of the Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 1–479（479 aa） Chain B 1–479（479 aa） Chain C 1–479（479 aa）	Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.49 Å
8YNN Structure of the Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–479（479 aa） Chain B 1–479（479 aa） Chain C 1–479（479 aa）	Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.97 Å

33 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CASP8_HUMAN
Isoform	Q14790-9
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–263； UniProt 276–538 Author chain B； PDBConstruct 1–263； UniProt 276–538 Author chain C； PDBConstruct 1–263； UniProt 276–538 Author chain D； PDBConstruct 1–263； UniProt 276–538 Author chain E； PDBConstruct 1–263； UniProt 276–538 Author chain F； PDBConstruct 1–263； UniProt 276–538

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	6px9
Deposition date deposition_date	2019-07-25
Structure title title	Crystal structure of procaspase-8 in complex with covalent small molecule inhibitor 63-R
Keywords keywords	zymogen, procaspase, covalent inhibitor, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	41.09 Å
Radius of gyration Rg (electron density) rg_electron	40.28 Å
Forward intensity I(0) i0	295011000.00
Molecular weight molecular_weight	140540.0 kDa
Excluded volume excluded_volume	175580 Å³
Envelope volume envelope_volume	236070 Å³
Hydration-shell volume shell_volume	47988 Å³
Envelope diameter envelope_diameter	126.8 Å
Shell Rg shell_rg	47.41 Å
Envelope Rg envelope_rg	38.77 Å
Shape Rg shape_rg	40.28 Å
Total Rg total_rg	40.65 Å
Total atoms total_atoms	9871
Residues n_residues	1251
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	126.0 Å
Rg (real space) rg_real	40.91 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	2.9500e+08
I(0) uncertainty (real space) i0_real_error	4.5990e+06
Rg (reciprocal space) rg_reciprocal	41.09 Å
I(0) (reciprocal space) i0_reciprocal	295100000.0000
Solution quality estimate total_estimate	0.8257
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	63.0 Å
Skewness Skewness skewness	-0.042
Kurtosis Kurtosis kurtosis	-0.823
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	25800000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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-8
Molecular weight formula_weight	31196.3 kDa
EC 编号 ec_number	3.4.22.61
Mutation mutation	D374A, D384A, C409S, C433S
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	9878

SESQTLDKVYQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHDDCTVEQIYEILKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVFFIQACQGDNYQKGIPVETASEEQPYLEMALSSPQTRYIPDEADFLLGMATVNNSVSYRNPAEGTWYIQSLCQSLRERSPRGDDILTILTEVNYEVSNKDDKKNMGKQMPQPTFTLRKKLVFPSDAAALEHHHHHH

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 non-polymer

Description description	N-{(3R)-1-[4-(morpholin-4-yl)benzene-1-carbonyl]piperidin-3-yl}-N-phenylacetamide
Molecular weight formula_weight	407.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6px9a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.17 — Caspase-like
Superfamily Superfamily superfamily	c.17.1 — Caspase-like
Family Family family	c.17.1.1 — Caspase catalytic domain

Domain ID domain_id	d6px9b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.17 — Caspase-like
Superfamily Superfamily superfamily	c.17.1 — Caspase-like
Family Family family	c.17.1.1 — Caspase catalytic domain

Domain ID domain_id	d6px9c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.17 — Caspase-like
Superfamily Superfamily superfamily	c.17.1 — Caspase-like
Family Family family	c.17.1.1 — Caspase catalytic domain

Domain ID domain_id	d6px9d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.17 — Caspase-like
Superfamily Superfamily superfamily	c.17.1 — Caspase-like
Family Family family	c.17.1.1 — Caspase catalytic domain

Domain ID domain_id	d6px9e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.17 — Caspase-like
Superfamily Superfamily superfamily	c.17.1 — Caspase-like
Family Family family	c.17.1.1 — Caspase catalytic domain

Domain ID domain_id	d6px9f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.17 — Caspase-like
Superfamily Superfamily superfamily	c.17.1 — Caspase-like
Family Family family	c.17.1.1 — Caspase catalytic domain

CATH v4.4 (6 domains)

Domain ID domain_id	6px9A00
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	6px9B00
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	6px9C00
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	6px9D00
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	6px9E00
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	6px9F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1460 —

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8. Citations (1)

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Unit-cell length a length_a	101.311 Å
Unit-cell length b length_b	101.311 Å
Unit-cell length c length_c	175.547 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	18

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.880 Å
Low-resolution limit resolution_low	35.100 Å
R factor r_factor	0.2894
R_work r_work	0.2856
R_free r_free	0.3665

fit	/app/data/saxs_computation/px/6px9/6px9.fit
pddf	/app/data/pr_computation/px/6px9/6px9.pr.out
profile	/app/data/saxs_computation/px/6px9/6px9.dat