SAXSdb — 1pyo

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

Caspase-2

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 167–333 Chain B； UniProt 348–452 Chain C； UniProt 167–333 Chain D； UniProt 348–452	Fragment：subunit p18, sequence database residues 151-316 Fragment：subunit p12, sequence database residues 331-435	ACETYL-LEU-ASP-GLU-SER-ASJ × 2 （P36114）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG 6000, MOPS, DTT, SUCROSE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.65 Å R-free 0.213

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 1PYO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2P2C Inhibition of caspase-2 by a designed ankyrin repeat protein (DARPin) Deposited 2007-03-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 167–333（167 aa） Fragment：Residues 167-333 Chain B 348–452（105 aa） Fragment：Residues 348-452 Chain C 167–333（167 aa） Fragment：Residues 167-333 Chain D 348–452（105 aa） Fragment：Residues 348-452	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；17% PEG 5000-MME, 0.1 M Tris-HOAc, 0.1 M KSCN, 30% ethylene glycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.24 Å R-free 0.305
2P2C Inhibition of caspase-2 by a designed ankyrin repeat protein (DARPin) Deposited 2007-03-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 167–333（167 aa） Fragment：Residues 167-333 Chain F 348–452（105 aa） Fragment：Residues 348-452 Chain G 167–333（167 aa） Fragment：Residues 167-333 Chain H 348–452（105 aa） Fragment：Residues 348-452	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；17% PEG 5000-MME, 0.1 M Tris-HOAc, 0.1 M KSCN, 30% ethylene glycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.24 Å R-free 0.305
2P2C Inhibition of caspase-2 by a designed ankyrin repeat protein (DARPin) Deposited 2007-03-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 167–333（167 aa） Fragment：Residues 167-333 Chain J 348–452（105 aa） Fragment：Residues 348-452 Chain K 167–333（167 aa） Fragment：Residues 167-333 Chain L 348–452（105 aa） Fragment：Residues 348-452	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；17% PEG 5000-MME, 0.1 M Tris-HOAc, 0.1 M KSCN, 30% ethylene glycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.24 Å R-free 0.305
3R5J Crystal structure of active caspase-2 bound with Ac-ADVAD-CHO Deposited 2011-03-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 175–333（159 aa） Chain B 349–452（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.77 Å R-free 0.218
3R5J Crystal structure of active caspase-2 bound with Ac-ADVAD-CHO Deposited 2011-03-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 175–333（159 aa） Chain D 349–452（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.77 Å R-free 0.218
3R5J Crystal structure of active caspase-2 bound with Ac-ADVAD-CHO Deposited 2011-03-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 175–333（159 aa） Chain B 349–452（104 aa） Chain C 175–333（159 aa） Chain D 349–452（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.77 Å R-free 0.218
3R6G Crystal structure of active caspase-2 bound with Ac-VDVAD-CHO Deposited 2011-03-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 175–333（159 aa） Chain B 349–452（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.07 Å R-free 0.210
3R6G Crystal structure of active caspase-2 bound with Ac-VDVAD-CHO Deposited 2011-03-21	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 175–333（159 aa） Chain D 349–452（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.07 Å R-free 0.210
3R6G Crystal structure of active caspase-2 bound with Ac-VDVAD-CHO Deposited 2011-03-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 175–333（159 aa） Chain B 349–452（104 aa） Chain C 175–333（159 aa） Chain D 349–452（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.07 Å R-free 0.210
3R6L Caspase-2 T380A bound with Ac-VDVAD-CHO Deposited 2011-03-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 175–333（159 aa） Chain B 349–452（104 aa）	Mutation：T380A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.194
3R6L Caspase-2 T380A bound with Ac-VDVAD-CHO Deposited 2011-03-21	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 175–333（159 aa） Chain D 349–452（104 aa）	Mutation：T380A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.194
3R6L Caspase-2 T380A bound with Ac-VDVAD-CHO Deposited 2011-03-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 175–333（159 aa） Chain B 349–452（104 aa） Chain C 175–333（159 aa） Chain D 349–452（104 aa）	Mutation：T380A Mutation：T380A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.194
3R7B Caspase-2 bound to one copy of Ac-DVAD-CHO Deposited 2011-03-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 175–333（159 aa） Chain B 349–452（104 aa） Chain C 175–333（159 aa） Chain D 349–452（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES (pH 7.0), 15% PEG 3350, 3mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.217
3R7N Caspase-2 bound with two copies of Ac-DVAD-CHO Deposited 2011-03-22	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 175–333（159 aa） Chain B 349–452（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.33 Å R-free 0.227
3R7N Caspase-2 bound with two copies of Ac-DVAD-CHO Deposited 2011-03-22	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 175–333（159 aa） Chain D 349–452（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.33 Å R-free 0.227
3R7N Caspase-2 bound with two copies of Ac-DVAD-CHO Deposited 2011-03-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 175–333（159 aa） Chain B 349–452（104 aa） Chain C 175–333（159 aa） Chain D 349–452（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.33 Å R-free 0.227
3R7S Crystal Structure of Apo Caspase2 Deposited 2011-03-22	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 175–333（159 aa） Fragment：UNP residues 175-333 Chain B 349–452（104 aa） Fragment：UNP residues 349-452	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.25 Å R-free 0.226
3R7S Crystal Structure of Apo Caspase2 Deposited 2011-03-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 175–333（159 aa） Fragment：UNP residues 175-333 Chain D 349–452（104 aa） Fragment：UNP residues 349-452	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.25 Å R-free 0.226
3R7S Crystal Structure of Apo Caspase2 Deposited 2011-03-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 175–333（159 aa） Fragment：UNP residues 175-333 Chain B 349–452（104 aa） Fragment：UNP residues 349-452 Chain C 175–333（159 aa） Fragment：UNP residues 175-333 Chain D 349–452（104 aa） Fragment：UNP residues 349-452	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.25 Å R-free 0.226
3RJM CASPASE2 IN COMPLEX WITH CHDI LIGAND 33c Deposited 2011-04-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 167–333（167 aa） Fragment：Residues 167-333 Chain B 348–452（105 aa） Fragment：Residues 348-452 Chain C 167–333（167 aa） Fragment：Residues 167-333 Chain D 348–452（105 aa） Fragment：Residues 348-452	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；26% PEG 3500, 100MM MES PH 6.5 - PH 7.0, SITTING DROP, VAPOR DIFFUSION, TEMPERATURE 290K, VAPOR DIFFUSION, SITTING DROP	Resolution 2.55 Å R-free 0.249
6S9K Structure of 14-3-3 gamma in complex with caspase-2 peptide containing 14-3-3 binding motif Ser139 and NLS Deposited 2019-07-15	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 B 135–168（34 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CFH 1,1,1,3,3,3-hexafluoropropan-2-ol × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；PEG 400, calcium chloride, HEPES, 1,1,1,3,3,3-hexafluoropropan-2-ol	Resolution 1.60 Å R-free 0.221
6SAD Structure of 14-3-3 gamma in complex with double phosphorylated caspase-2 peptide on Ser139 and Ser164 Deposited 2019-07-16	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 C 135–168（34 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；PEG 400, magnesium chloride, HEPES, 1,1,1,3,3,3-hexafluoropropan-2-ol	Resolution 2.75 Å R-free 0.271
8VP4 Crystal Structure of JF1cpCasp2 with Peptide Inhibitor AcVDVAD-CHO Deposited 2024-01-16	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 334–448（115 aa） Chain A 176–333（158 aa） Chain B 334–448（115 aa） Chain B 176–333（158 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris, pH 8.0, 0.2 M Sodium chloride, 20% w/v PEG 6000	Resolution 1.51 Å R-free 0.214
9C2Y Crystal Structure of JF1cpCasp2 in complex with MUR-65 Deposited 2024-05-31	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 334–448（115 aa） Chain A 177–333（157 aa） Chain B 334–448（115 aa） Chain B 177–333（157 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Tris, pH 8.0, 0.2 M Sodium chloride, 20% w/v PEG 6000	Resolution 1.96 Å R-free 0.248
9C2Y Crystal Structure of JF1cpCasp2 in complex with MUR-65 Deposited 2024-05-31	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 334–448（115 aa） Chain C 177–333（157 aa） Chain D 334–448（115 aa） Chain D 177–333（157 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Tris, pH 8.0, 0.2 M Sodium chloride, 20% w/v PEG 6000	Resolution 1.96 Å R-free 0.248

12 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CASP2_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–167； UniProt 167–333 Author chain C； PDBConstruct 1–167； UniProt 167–333 Author chain B； PDBConstruct 1–105； UniProt 348–452 Author chain D； PDBConstruct 1–105； UniProt 348–452

ACETYL-LEU-ASP-GLU-SER-ASJ

OrganismNot specified

UniProt P36114

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 E； UniProt 54–58 Chain F； UniProt 54–58	Non-standard monomer：Yes (specific site not provided by mmCIF)	Caspase-2 × 2 （P42575） Caspase-2 × 2 （P42575）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG 6000, MOPS, DTT, SUCROSE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.65 Å R-free 0.213

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	YKZ8_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 2–6； UniProt 54–58 Author chain F； PDBConstruct 2–6； UniProt 54–58

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1pyo
Deposition date deposition_date	2003-07-09
Structure title title	Crystal Structure of Human Caspase-2 in Complex with Acetyl-Leu-Asp-Glu-Ser-Asp-cho
Keywords keywords	APOPTOSIS, CASPASE, ALPHA-BETA, THIOL PROTEASE, 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	23.79 Å
Radius of gyration Rg (electron density) rg_electron	22.66 Å
Forward intensity I(0) i0	61263700.00
Molecular weight molecular_weight	59721.0 kDa
Excluded volume excluded_volume	74176 Å³
Envelope volume envelope_volume	85545 Å³
Hydration-shell volume shell_volume	30167 Å³
Envelope diameter envelope_diameter	72.1 Å
Shell Rg shell_rg	30.66 Å
Envelope Rg envelope_rg	22.87 Å
Shape Rg shape_rg	22.68 Å
Total Rg total_rg	23.45 Å
Total atoms total_atoms	4181
Residues n_residues	525
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	70.8 Å
Rg (real space) rg_real	23.59 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	6.1260e+07
I(0) uncertainty (real space) i0_real_error	7.2990e+05
Rg (reciprocal space) rg_reciprocal	23.64 Å
I(0) (reciprocal space) i0_reciprocal	61270000.0000
Solution quality estimate total_estimate	0.9076
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.0 Å
Skewness Skewness skewness	0.032
Kurtosis Kurtosis kurtosis	-0.579
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11090000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.974

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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-2
Molecular weight formula_weight	18790.3 kDa
EC 编号 ec_number	3.4.22.-
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	4606

NKDGPVCLQVKPCTPEFYQTHFQLAYRLQSRPRGLALVLSNVHFTGEKELEFRSGGDVDHSTLVTLFKLLGYDVHVLCDQTAQEMQEKLQNFAQLPAHRVTDSCIVALLSHGVEGAIYGVDGKLLQLQEVFQLFDNANCPSLQNKPKMFFIQACRGDETDRGVDQQD

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-2
Molecular weight formula_weight	11921.0 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AGKEKLPKMRLPTRSDMICGYACLKGTAAMRNTKRGSWYIEALAQVFSERACDMHVADMLVKVNALIKDREGYAPGTEFHRCKEMSEYCSTLCRHLYLFPGHPPT

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	ACETYL-LEU-ASP-GLU-SER-ASJ
Molecular weight formula_weight	589.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

XLDESX

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	385

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1pyo.1
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	d1pyo.2
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 (4 domains)

Domain ID domain_id	1pyoA00
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	1pyoB00
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	1pyoC00
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	1pyoD00
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	63.649 Å
Unit-cell length b length_b	96.583 Å
Unit-cell length c length_c	97.547 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.1890
R_free r_free	0.2130

fit	/app/data/saxs_computation/py/1pyo/1pyo.fit
pddf	/app/data/pr_computation/py/1pyo/1pyo.pr.out
profile	/app/data/saxs_computation/py/1pyo/1pyo.dat

Crystal Structure of Human Caspase-2 in Complex with Acetyl-Leu-Asp-Glu-Ser-Asp-cho

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

Caspase-2

State in the Current Structure

Other States of the Same Protein in the Database

ACETYL-LEU-ASP-GLU-SER-ASJ

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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)