SAXSdb — 6nry

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

Caspase-4

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 92–377	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；25mM Bis-Tris, 20% PEG3350	Resolution 2.18 Å R-free 0.237

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 6NRY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6KMZ caspase-4 P22/P10 C258A in complex with human GSDMD-C domain Deposited 2019-08-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 105–289（185 aa） Chain B 105–289（185 aa） Chain a 290–377（88 aa） Chain b 290–377（88 aa）	Mutation：C258A Mutation：C258A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris-HCl pH 7.5, 200 mM sodium tartrate, 20% (w/v) polyethylene glycol 3350, 5% glycerol and 4% 1,1,1,3,3,3-hexafluoro-2-propanol	Resolution 3.61 Å R-free 0.319
6KMZ caspase-4 P22/P10 C258A in complex with human GSDMD-C domain Deposited 2019-08-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 105–289（185 aa） Chain D 105–289（185 aa） Chain c 290–377（88 aa） Chain d 290–377（88 aa）	Mutation：C258A Mutation：C258A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris-HCl pH 7.5, 200 mM sodium tartrate, 20% (w/v) polyethylene glycol 3350, 5% glycerol and 4% 1,1,1,3,3,3-hexafluoro-2-propanol	Resolution 3.61 Å R-free 0.319
7WR0 P32 of caspase-4 C258A mutant Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 102–377（276 aa）	Mutation：C258A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2 M potassium chloride	Resolution 2.80 Å R-free 0.266
7WR1 P32 of caspase-4 C258A mutant in complex with OspC3 C-terminal ankyrin-repeat domain Deposited 2022-01-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 102–377（276 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；5% PEG8000, 0.1M Tris-HCl pH 7.5, % 2-propanol	Resolution 2.13 Å R-free 0.200
7WR1 P32 of caspase-4 C258A mutant in complex with OspC3 C-terminal ankyrin-repeat domain Deposited 2022-01-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 102–377（276 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；5% PEG8000, 0.1M Tris-HCl pH 7.5, % 2-propanol	Resolution 2.13 Å R-free 0.200
7WR4 Crystal structure of OspC3-calmodulin-caspase-4 complex Deposited 2022-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 102–377（276 aa）	Mutation：C258A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 0.1 M HEPES pH 7.4, 0.2 M Ammonium sulfate, 0.3 M NDSB-195	Resolution 2.75 Å R-free 0.270
7WR5 Crystal structure of OspC3-calmodulin-caspase-4 complex binding with 2'-aF-NAD+ Deposited 2022-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 102–377（276 aa）	Mutation：C258A	5ZV [[(2~{R},3~{R},4~{S},5~{R})-5-(3-aminocarbonylpyridin-1-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2 M Potassium acetate	Resolution 3.10 Å R-free 0.272
7WR6 Crystal structure of ADP-riboxanated caspase-4 in complex with Af1521 Deposited 2022-01-26	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 102–377（276 aa）	Mutation：C258A	5ZY [[(3~{a}~{S},5~{R},6~{R},6~{a}~{R})-2-azanylidene-3-[(4~{R})-4-azanyl-5-oxidanylidene-pentyl]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxazol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；27% PEG 3350, 0.05M CAPSO pH 9.0	Resolution 1.96 Å R-free 0.228
8J6K Crystal structure of pro-interleukin-18 and caspase-4 complex Deposited 2023-04-26	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 A 102–270（169 aa） Chain a 290–377（88 aa）	Mutation：C258A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Calcium acetate, 0.1M Tris-HCl pH 9.0, 13% PEG 8000, 0.01 M L-Glutathione reduced, 0.01 M L-Glutathione oxidized	Resolution 3.12 Å R-free 0.269
8SPB Caspase-4/Pro-IL-18 complex Deposited 2023-05-02	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 × 6 PDB declaration: hexameric	Chain A 94–270（177 aa） Chain B 290–377（88 aa） Chain a 94–270（177 aa） Chain b 290–377（88 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

8 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CASP4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–288； UniProt 92–377

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	6nry
Deposition date deposition_date	2019-01-24
Structure title title	Crystal structure of human caspase-4
Keywords keywords	inflammation, caspase, pyroptosis, enzyme, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	19.43 Å
Radius of gyration Rg (electron density) rg_electron	18.15 Å
Forward intensity I(0) i0	14328200.00
Molecular weight molecular_weight	28382.0 kDa
Excluded volume excluded_volume	35496 Å³
Envelope volume envelope_volume	41500 Å³
Hydration-shell volume shell_volume	19019 Å³
Envelope diameter envelope_diameter	65.0 Å
Shell Rg shell_rg	24.60 Å
Envelope Rg envelope_rg	18.56 Å
Shape Rg shape_rg	18.15 Å
Total Rg total_rg	19.07 Å
Total atoms total_atoms	1992
Residues n_residues	245
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	64.5 Å
Rg (real space) rg_real	19.32 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.4330e+07
I(0) uncertainty (real space) i0_real_error	1.7830e+05
Rg (reciprocal space) rg_reciprocal	19.34 Å
I(0) (reciprocal space) i0_reciprocal	14330000.0000
Solution quality estimate total_estimate	0.7337
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.182
Kurtosis Kurtosis kurtosis	-0.365
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2629000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 0.356; Positv: 1.000; Valcen: 0.999; Smooth: 0.987

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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-4
Molecular weight formula_weight	32826.1 kDa
EC 编号 ec_number	3.4.22.57
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2067

GSMEAGPPESGESTDALKLCPHEEFLRLCKERAEEIYPIKERNNRTRLALIICNTEFDHLPPRNGADFDITGMKELLEGLDYSVDVEENLTARDMESALRAFATRPEHKSSDSTFLVLMSHGILEGICGTVHDEKKPDVLLYDTIFQIFNNRNCLSLKDKPKVIIVQAARGANRGELWVRDSPASLEVASSQSSENLEEDAVYKTHVEKDFIAFCSSTPHNVSWRDSTMGSIFITQLITCFQKYSWCCHLEEVFRKVQQSFETPRAKAQMPTIERLSMTRYFYLFPGN

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	GLYCEROL
Molecular weight formula_weight	92.1 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	75

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6nryA01
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	40.687 Å
Unit-cell length b length_b	163.383 Å
Unit-cell length c length_c	103.661 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.184 Å
Low-resolution limit resolution_low	27.592 Å
R factor r_factor	0.1990
R_work r_work	0.1947
R_free r_free	0.2367

fit	/app/data/saxs_computation/nr/6nry/6nry.fit
pddf	/app/data/pr_computation/nr/6nry/6nry.pr.out
profile	/app/data/saxs_computation/nr/6nry/6nry.dat

Crystal structure of human caspase-4

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

Caspase-4

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