SAXSdb — 6ao4

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

Gasdermin-D

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 277–484	Fragment：unp residues 277-484	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；2.1 M DL-malic acid, pH 7.0	Resolution 2.90 Å R-free 0.290

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 6AO4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5NH1 Structure of the C-terminal domain of human Gasdermin D Deposited 2017-03-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 278–484（207 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；303 K；1.229 M NaCitrate, HEPES, pH 7.25	Resolution 2.04 Å R-free 0.264
5WQT Structure of a protein involved in pyroptosis Deposited 2016-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 276–484（209 aa） Fragment：C-terminal (UNP RESIDUES 276-484) Chain B 276–484（209 aa） Fragment：C-terminal (UNP RESIDUES 276-484)	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 3 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；291 K；20mM Sodium bromide, 0.1M Hepes sodium pH7.0, 1.5M Sodium citrate tribasic dihydrate	Resolution 2.64 Å R-free 0.286
6KMZ caspase-4 P22/P10 C258A in complex with human GSDMD-C domain Deposited 2019-08-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 287–480（194 aa）	Not recorded	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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 286–480（195 aa）	Not recorded	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
6KN0 caspase-1 P20/P10 C285A in complex with human GSDMD-C domain Deposited 2019-08-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 283–480（198 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；150 mM KBr, 30% (w/v) polyethylene glycol mono-methyester 2000	Resolution 2.79 Å R-free 0.300
6KN0 caspase-1 P20/P10 C285A in complex with human GSDMD-C domain Deposited 2019-08-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 283–480（198 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；150 mM KBr, 30% (w/v) polyethylene glycol mono-methyester 2000	Resolution 2.79 Å R-free 0.300
6N9O Crystal structure of human GSDMD Deposited 2018-12-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–484（484 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25% PEG3350, 0.1M Bis-Tris pH 5.5, 200 mM NaCl, and 10 mM DTT	Resolution 3.50 Å R-free 0.345
6N9O Crystal structure of human GSDMD Deposited 2018-12-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–484（484 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25% PEG3350, 0.1M Bis-Tris pH 5.5, 200 mM NaCl, and 10 mM DTT	Resolution 3.50 Å R-free 0.345
6N9O Crystal structure of human GSDMD Deposited 2018-12-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–484（484 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25% PEG3350, 0.1M Bis-Tris pH 5.5, 200 mM NaCl, and 10 mM DTT	Resolution 3.50 Å R-free 0.345
6N9O Crystal structure of human GSDMD Deposited 2018-12-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–484（484 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25% PEG3350, 0.1M Bis-Tris pH 5.5, 200 mM NaCl, and 10 mM DTT	Resolution 3.50 Å R-free 0.345
6VFE Gasdermin D pore Deposited 2020-01-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 33 PDB declaration: 33-meric	Chain A 1–241（241 aa） Chain B 1–241（241 aa） Chain C 1–241（241 aa） Chain D 1–241（241 aa） Chain E 1–241（241 aa） Chain F 1–241（241 aa） Chain G 1–241（241 aa） Chain H 1–241（241 aa） Chain I 1–241（241 aa） Chain J 1–241（241 aa） Chain K 1–241（241 aa） Chain L 1–241（241 aa） Chain M 1–241（241 aa） Chain N 1–241（241 aa） Chain O 1–241（241 aa） Chain P 1–241（241 aa） Chain Q 1–241（241 aa） Chain R 1–241（241 aa） Chain S 1–241（241 aa） Chain T 1–241（241 aa） Chain U 1–241（241 aa） Chain V 1–241（241 aa） Chain W 1–241（241 aa） Chain X 1–241（241 aa） Chain Y 1–241（241 aa） Chain Z 1–241（241 aa） Chain a 1–241（241 aa） Chain b 1–241（241 aa） Chain c 1–241（241 aa） Chain d 1–241（241 aa） Chain e 1–241（241 aa） Chain f 1–241（241 aa） Chain g 1–241（241 aa）	Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E Mutation：L192E	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7Z1X Crystal structure of human Gasdermin D complexed with nanobodies VHH-2 and VHH-6 Deposited 2022-02-25	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 1–484（484 aa） Chain D 1–484（484 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.4；293 K；20 mg/ml protein complex; 0.04 M NaCl, 25.8% (v/v) PEG400, 0.05 M Na3Cit pH 4.4	Resolution 1.86 Å R-free 0.249
9E0V GSDMD bound to a peptide Deposited 2024-10-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 276–484（209 aa） Fragment：MBP + GSD (UNP residues 276-484)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289.15 K；0.1 M HEPES, pH 7.5, 1.25 M sodium citrate dihydrate, 20 mM TCEP	Resolution 1.64 Å R-free 0.212

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GSDMD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–209； UniProt 277–484

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	6ao4
Deposition date deposition_date	2017-08-15
Structure title title	Crystal structure of the human gasdermin D C-terminal domain
Keywords keywords	Inflammasome, pyroptosis, gasdermin D, autoinhibition, Salmonella infection, 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	18.51 Å
Radius of gyration Rg (electron density) rg_electron	17.22 Å
Forward intensity I(0) i0	7679420.00
Molecular weight molecular_weight	20611.0 kDa
Excluded volume excluded_volume	25994 Å³
Envelope volume envelope_volume	30944 Å³
Hydration-shell volume shell_volume	15451 Å³
Envelope diameter envelope_diameter	62.1 Å
Shell Rg shell_rg	22.91 Å
Envelope Rg envelope_rg	17.62 Å
Shape Rg shape_rg	17.23 Å
Total Rg total_rg	18.20 Å
Total atoms total_atoms	1445
Residues n_residues	192
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	61.6 Å
Rg (real space) rg_real	18.49 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	7.6790e+06
I(0) uncertainty (real space) i0_real_error	9.8230e+04
Rg (reciprocal space) rg_reciprocal	18.50 Å
I(0) (reciprocal space) i0_reciprocal	7679000.0000
Solution quality estimate total_estimate	0.7959
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	54.9 Å
Skewness Skewness skewness	0.356
Kurtosis Kurtosis kurtosis	-0.190
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1659000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	47.750 Å
Unit-cell length b length_b	108.540 Å
Unit-cell length c length_c	45.910 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.901 Å
Low-resolution limit resolution_low	35.050 Å
R factor r_factor	0.2360
R_work r_work	0.2321
R_free r_free	0.2897

Description description	Gasdermin-D
Molecular weight formula_weight	22354.4 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	1445

Crystal structure of the human gasdermin D C-terminal domain

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

Gasdermin-D

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

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

fit	/app/data/saxs_computation/ao/6ao4/6ao4.fit
pddf	/app/data/pr_computation/ao/6ao4/6ao4.pr.out
profile	/app/data/saxs_computation/ao/6ao4/6ao4.dat