SAXSdb — 3h13

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

CASP8 and FADD-like apoptosis regulator

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 209–480	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；0.1 M Mes, 18% PEG, 5000 monomethyl ether, 0.1 M ammonium sulfate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.20 Å R-free 0.220

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 3H13	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2N5R NMR structure of cFLIP-derived calmodulin binding peptide Deposited 2015-07-24	Different construct 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 62–73（12 aa） Fragment：DED 1 domain residues 62-73	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；288 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition 20 mM potassium phosphate, 150 mM sodium chloride, 1 mM calcium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3H11 Zymogen caspase-8:c-FLIPL protease domain complex Deposited 2009-04-10	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 209–480（272 aa）	Not recorded	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
6M6O NMR SOLUTION STRUCTURE OF A C-FLIPs Deposited 2020-03-16	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 2–173（172 aa）	Mutation：F114G	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 110；Pressure 1 NMR sample composition 0.6 nM [U-99% 13C; U-99% 15N] c-FLIPS, 1.0 nM EDTA-Na2, 1.0 nM TCEP, 0.02 % NaN3, 60 nM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7DEE Structural Basis of the regulation of DISC Assembly by the interaction of c-FLIPs with Procaspase-8 Deposited 2020-11-03	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–173（172 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 110；Pressure 1 NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 60；Pressure 1 NMR sample composition 10 mM C8-H1a, 0.002 % v/v sodium azide, 110 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 04 mM C8-H1a, 0.002 % v/v sodium azide, 110 mM sodium phosphate, 0.6 mM [U-99% 13C; U-99% 15N] c-FLIPs, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.002 % v/v sodium azide, 110 mM sodium phosphate, 0.6 mM [U-99% 13C; U-99% 15N] c-FLIPs, 1 mM TCEP, 1 mM EDTA, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
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 H 1–181（181 aa） Chain I 1–181（181 aa） Chain J 1–181（181 aa） Chain K 1–181（181 aa）	Not recorded	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 G 1–181（181 aa） Chain H 1–181（181 aa） Chain I 1–181（181 aa） Chain K 1–181（181 aa）	Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G 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 H 1–181（181 aa） Chain I 1–181（181 aa） Chain J 1–181（181 aa） Chain K 1–181（181 aa）	Mutation：H7G Mutation：H7G Mutation：H7G Mutation：H7G	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 F 1–181（181 aa） Chain G 1–181（181 aa） Chain H 1–181（181 aa） Chain I 1–181（181 aa） Chain J 1–181（181 aa） Chain K 1–181（181 aa）	Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G 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 F 1–181（181 aa） Chain G 1–181（181 aa） Chain H 1–181（181 aa） Chain I 1–181（181 aa） Chain J 1–181（181 aa） Chain K 1–181（181 aa）	Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H7G 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 F 1–181（181 aa） Chain G 1–181（181 aa） Chain H 1–181（181 aa） Chain I 1–181（181 aa） Chain J 1–181（181 aa） Chain K 1–181（181 aa） Chain M 1–181（181 aa） Chain N 1–181（181 aa） Chain O 1–181（181 aa）	Not recorded	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 G 1–181（181 aa） Chain H 1–181（181 aa） Chain I 1–181（181 aa） Chain J 1–181（181 aa） Chain K 1–181（181 aa）	Not recorded	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 G 1–181（181 aa） Chain H 1–181（181 aa） Chain I 1–181（181 aa） Chain J 1–181（181 aa） Chain K 1–181（181 aa）	Not recorded	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 F 1–181（181 aa） Chain G 1–181（181 aa） Chain H 1–181（181 aa） Chain I 1–181（181 aa） Chain J 1–181（181 aa） Chain K 1–181（181 aa）	Not recorded	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 F 1–181（181 aa） Chain G 1–181（181 aa） Chain H 1–181（181 aa） Chain I 1–181（181 aa） Chain J 1–181（181 aa） Chain K 1–181（181 aa） Chain N 1–181（181 aa） Chain O 1–181（181 aa）	Not recorded	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 H 1–181（181 aa） Chain I 1–181（181 aa） Chain J 1–181（181 aa） Chain K 1–181（181 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.97 Å

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

View Construct and Data Evidence

UniProt name	CFLAR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–272； UniProt 209–480

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	3h13
Deposition date deposition_date	2009-04-10
Structure title title	c-FLIPL protease-like domain
Keywords keywords	cFLIP-L, dimer, cell death, Alternative splicing, Apoptosis, Host-virus interaction, Polymorphism; APOPTOSIS
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	17.99 Å
Radius of gyration Rg (electron density) rg_electron	16.54 Å
Forward intensity I(0) i0	10546300.00
Molecular weight molecular_weight	24268.0 kDa
Excluded volume excluded_volume	30451 Å³
Envelope volume envelope_volume	34271 Å³
Hydration-shell volume shell_volume	17119 Å³
Envelope diameter envelope_diameter	57.4 Å
Shell Rg shell_rg	22.97 Å
Envelope Rg envelope_rg	16.91 Å
Shape Rg shape_rg	16.54 Å
Total Rg total_rg	17.61 Å
Total atoms total_atoms	1704
Residues n_residues	208
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	57.5 Å
Rg (real space) rg_real	17.86 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.0550e+07
I(0) uncertainty (real space) i0_real_error	1.1880e+05
Rg (reciprocal space) rg_reciprocal	17.88 Å
I(0) (reciprocal space) i0_reciprocal	10550000.0000
Solution quality estimate total_estimate	0.8880
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.134
Kurtosis Kurtosis kurtosis	-0.380
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2521000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3h13a_
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 (1 domains)

Domain ID domain_id	3h13A00
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	101.940 Å
Unit-cell length b length_b	101.940 Å
Unit-cell length c length_c	61.360 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	29.430 Å
R factor r_factor	0.1870
R_work r_work	0.1870
R_free r_free	0.2200

Description description	CASP8 and FADD-like apoptosis regulator
Molecular weight formula_weight	31450.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1780

c-FLIPL protease-like domain

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

CASP8 and FADD-like apoptosis regulator

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

fit	/app/data/saxs_computation/h1/3h13/3h13.fit
pddf	/app/data/pr_computation/h1/3h13/3h13.pr.out
profile	/app/data/saxs_computation/h1/3h13/3h13.dat