SAXSdb — 2ar9

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

Caspase-9

OrganismNot specified

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 140–416 Chain B； UniProt 140–416	Fragment：residues 140-416 Mutation：C287S, G402C, C403I, F404V, N405S, F406M	MLT D-MALATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；PEG5000 monomethylether, MES, tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.80 Å R-free 0.288
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 140–416 Chain D； UniProt 140–416	Fragment：residues 140-416 Mutation：C287S, G402C, C403I, F404V, N405S, F406M	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；PEG5000 monomethylether, MES, tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.80 Å R-free 0.288

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 2AR9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NW9 STRUCTURE OF CASPASE-9 IN AN INHIBITORY COMPLEX WITH XIAP-BIR3 Deposited 2003-02-05	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 B 140–416（277 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Tris, potassium phosphate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.235
3D9T CIAP1-BIR3 in complex with N-terminal peptide from Caspase-9 (ATPFQE) Deposited 2008-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 316–321（6 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.1M NA FORMATE,10% GLYCEROL,1.5MM PEPTIDE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.205
3D9T CIAP1-BIR3 in complex with N-terminal peptide from Caspase-9 (ATPFQE) Deposited 2008-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 316–321（6 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.1M NA FORMATE,10% GLYCEROL,1.5MM PEPTIDE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.205
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3V3K Human caspase 9 in complex with bacterial effector protein Deposited 2011-12-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 141–416（276 aa） Fragment：UNP Residues 141-416	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.75 K-Na-Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.49 Å R-free 0.259
3YGS APAF-1 CARD IN COMPLEX WITH PRODOMAIN OF PROCASPASE-9 Deposited 1999-05-08	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 P 1–96（96 aa） Fragment：PRODOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.50 Å R-free 0.299
4RHW Crystal structure of Apaf-1 CARD and caspase-9 CARD complex Deposited 2014-10-03	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 E 1–100（100 aa） Fragment：card domain Chain F 1–100（100 aa） Fragment：card domain	Not recorded	SO4 SULFATE ION × 7 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；13% PEG 3000, 0.2M ammonium sulfate, 0.1M MES (pH5.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.226
5JUY Active human apoptosome with procaspase-9 Deposited 2016-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain O 1–95（95 aa） Fragment：N-terminal caspase recognition domain Chain P 1–95（95 aa） Fragment：N-terminal caspase recognition domain Chain Q 1–95（95 aa） Fragment：N-terminal caspase recognition domain Chain R 1–95（95 aa） Fragment：N-terminal caspase recognition domain	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 HEC HEME C × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Buffer A cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
9R44 Crystal structure of human caspase-9 CARD Deposited 2025-05-07	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 1–99（99 aa） Chain E 1–99（99 aa） Chain H 1–99（99 aa） Chain L 1–99（99 aa）	Not recorded	SO4 SULFATE ION × 18 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.5 M Lithium sulfate, 0.1 M Sodium HEPES, and pH 7.5 Protein concentration: 15 mg/ml Buffer in: 20 mM Hepes, 50 mM NaCl, 2 mM TCEP, and pH 7.5	Resolution 2.46 Å R-free 0.265

7 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CASP9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–278； UniProt 140–416 Author chain B； PDBConstruct 2–278； UniProt 140–416 Author chain C； PDBConstruct 2–278； UniProt 140–416 Author chain D； PDBConstruct 2–278； UniProt 140–416

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	2ar9
Deposition date deposition_date	2005-08-19
Structure title title	Crystal structure of a dimeric caspase-9
Keywords keywords	caspase, caspase activation, initiator caspase, cysteine protease, engineered caspase-9, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	31.35 Å
Radius of gyration Rg (electron density) rg_electron	30.37 Å
Forward intensity I(0) i0	160572000.00
Molecular weight molecular_weight	102040.0 kDa
Excluded volume excluded_volume	128260 Å³
Envelope volume envelope_volume	154190 Å³
Hydration-shell volume shell_volume	41972 Å³
Envelope diameter envelope_diameter	110.6 Å
Shell Rg shell_rg	37.83 Å
Envelope Rg envelope_rg	30.29 Å
Shape Rg shape_rg	30.33 Å
Total Rg total_rg	31.15 Å
Total atoms total_atoms	7153
Residues n_residues	923
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	101.1 Å
Rg (real space) rg_real	31.29 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.6060e+08
I(0) uncertainty (real space) i0_real_error	2.3570e+06
Rg (reciprocal space) rg_reciprocal	31.32 Å
I(0) (reciprocal space) i0_reciprocal	160600000.0000
Solution quality estimate total_estimate	0.8973
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.7 Å
Skewness Skewness skewness	0.285
Kurtosis Kurtosis kurtosis	-0.466
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38010000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.967

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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-9
Molecular weight formula_weight	30553.8 kDa
EC 编号 ec_number	3.4.22.-
Mutation mutation	C287S, G402C, C403I, F404V, N405S, F406M
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7286

MGALESLRGNADLAYILSMEPCGHCLIINNVNFCRESGLRTRTGSNIDCEKLRRRFSSLHFMVEVKGDLTAKKMVLALLELARQDHGALDCCVVVILSHGCQASHLQFPGAVYGTDGCPVSVEKIVNIFNGTSCPSLGGKPKLFFIQASGGEQKDHGFEVASTSPEDESPGSNPEPDATPFQEGLRTFDQLDAISSLPTPSDIFVSYSTFPGFVSWRDPKSGSWYVETLDDIFEQWAHSEDLQSLLLRVANAVSVKGIYKQMPCIVSMLRKKLFFKTS

Entity 2 Entity 2 non-polymer

Description description	D-MALATE
Molecular weight formula_weight	134.1 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	133

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2ar9a_
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	d2ar9b_
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	d2ar9c_
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	d2ar9d_
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	2ar9A00
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	2ar9B00
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	2ar9C00
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	2ar9D00
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	144.698 Å
Unit-cell length b length_b	78.055 Å
Unit-cell length c length_c	125.963 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	11.000 Å
R factor r_factor	0.2400
R_work r_work	0.2370
R_free r_free	0.2880

fit	/app/data/saxs_computation/ar/2ar9/2ar9.fit
pddf	/app/data/pr_computation/ar/2ar9/2ar9.pr.out
profile	/app/data/saxs_computation/ar/2ar9/2ar9.dat

Crystal structure of a dimeric caspase-9

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

Caspase-9

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