SAXSdb — 3qf2

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

NACHT, LRR and PYD domains-containing protein 3

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 3–112	Fragment：PYD domain, DAPIN domain, residues 3-112	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M ammonium citrate, 0.1M sodium acetate pH4.6, 30% PEG MME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.235
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 3–112	Fragment：PYD domain, DAPIN domain, residues 3-112	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M ammonium citrate, 0.1M sodium acetate pH4.6, 30% PEG MME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.235

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 3QF2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NAQ 3D NMR solution structure of NLRP3 PYD Deposited 2016-01-07	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–93（91 aa） Fragment：Pyrin domain residues 3-93	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.6；303 K；Ionic strength (raw mmCIF value) 0.0051；Pressure ambient NMR sample composition 100-200 uM [U-13C; U-15N] protein, 5 mM [U-2H] TCEP, 100 uM sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6NPY Cryo-EM structure of NLRP3 bound to NEK7 Deposited 2019-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 3–1036（1034 aa）	Mutation：D133I, R135C, K136A, K140A	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7ALV Crystal Structure of NLRP3 NACHT domain in complex with a potent inhibitor Deposited 2020-10-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa） Fragment：NACHT domain	Not recorded	RM5 1-[4-chloranyl-2,6-di(propan-2-yl)phenyl]-3-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-urea × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M Hepes pH 7.5, 1.4M SodiumCitrate	Resolution 2.83 Å R-free 0.265
7PZC Cryo-EM structure of the NLRP3 decamer bound to the inhibitor CRID3 Deposited 2021-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 1–1036（1036 aa） Chain B 1–1036（1036 aa） Chain C 1–1036（1036 aa） Chain D 1–1036（1036 aa） Chain E 1–1036（1036 aa） Chain F 1–1036（1036 aa） Chain G 1–1036（1036 aa） Chain H 1–1036（1036 aa） Chain I 1–1036（1036 aa） Chain J 1–1036（1036 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 10 8GI 1-(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)-3-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-urea × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 10 mM MgCl2, 1 mM ADP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7PZD Cryo-EM structure of the NLRP3 PYD filament Deposited 2021-10-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain G 3–110（108 aa） Chain H 3–110（108 aa） Chain I 3–110（108 aa） Chain J 3–110（108 aa） Chain K 3–110（108 aa） Chain L 3–110（108 aa） Chain M 3–110（108 aa） Chain N 3–110（108 aa） Chain O 3–110（108 aa） Chain P 3–110（108 aa） Chain Q 3–110（108 aa） Chain R 3–110（108 aa） Chain S 3–110（108 aa） Chain T 3–110（108 aa） Chain U 3–110（108 aa） Chain V 3–110（108 aa） Chain W 3–110（108 aa） Chain X 3–110（108 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES (pH 7.5), 150 mM NaCl, 0.5 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7VTP Cryo-EM structure of PYD-deleted human NLRP3 hexamer Deposited 2021-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 130–1036（907 aa） Chain B 130–1036（907 aa） Chain C 130–1036（907 aa） Chain D 130–1036（907 aa） Chain E 130–1036（907 aa） Chain F 130–1036（907 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 7YN 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES-NaOH (pH 7.5), 0.2 M NaCl, 1 mM MgCl2, 0.5 mM TCEP, 1.0 mM ADP, 0.05 mM MCC950 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
7ZGU Human NLRP3-deltaPYD hexamer Deposited 2022-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 126–1036（911 aa） Chain B 126–1036（911 aa） Chain C 126–1036（911 aa） Chain D 126–1036（911 aa） Chain E 126–1036（911 aa） Chain F 126–1036（911 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8EJ4 Cryo-EM structure of the active NLRP3 inflammasome disk Deposited 2022-09-16	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 × 20 PDB declaration: eicosameric	Chain A 133–1034（902 aa） Chain B 133–1034（902 aa） Chain C 133–1034（902 aa） Chain D 133–1034（902 aa） Chain E 133–1034（902 aa） Chain F 133–1034（902 aa） Chain G 133–1034（902 aa） Chain H 133–1034（902 aa） Chain I 133–1034（902 aa） Chain J 133–1034（902 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 10 MG MAGNESIUM ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8ERT NLRP3 PYD filament Deposited 2022-10-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 21 PDB declaration: 21-meric	Chain A 1–95（95 aa） Chain B 1–95（95 aa） Chain C 1–95（95 aa） Chain D 1–95（95 aa） Chain E 1–95（95 aa） Chain F 1–95（95 aa） Chain G 1–95（95 aa） Chain I 1–95（95 aa） Chain J 1–95（95 aa） Chain K 1–95（95 aa） Chain L 1–95（95 aa） Chain M 1–95（95 aa） Chain N 1–95（95 aa） Chain O 1–95（95 aa） Chain Q 1–95（95 aa） Chain R 1–95（95 aa） Chain S 1–95（95 aa） Chain U 1–95（95 aa） Chain V 1–95（95 aa） Chain W 1–95（95 aa） Chain X 1–95（95 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8ETR CryoEM Structure of NLRP3 NACHT domain in complex with G2394 Deposited 2022-10-17	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–676（543 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 WTN (6S,8R)-N-[(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)carbamoyl]-6-(methylamino)-6,7-dihydro-5H-pyrazolo[5,1-b][1,3]oxazine-3-sulfonamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；0.15M NaCl, 20mM Tris pH 7.5, 10% glycerol, 1mM TCEP, 2.5mM ATP, 2mM MgCl2. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8RI2 Crystal structure of NLRP3 in complex with inhibitor NP3-562 Deposited 2023-12-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa）	Not recorded	A1H02 2-[4-chloranyl-9-oxidanylidene-12-(2-oxidanylpropan-2-yl)-5-thia-1,10,11-triazatricyclo[6.4.0.0^{2,6}]dodeca-2(6),3,7,11-tetraen-10-yl]-~{N}-[(3~{R})-1-methylpiperidin-3-yl]ethanamide × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；protein: well = 1: 1 well: 1.94 M Ammonium citrate pH 7.0 protein: 7 mg/ml protein copurified with 1 uM inhibitor	Resolution 2.80 Å R-free 0.270
8SWF Cryo-EM structure of NLRP3 open octamer Deposited 2023-05-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 130–1036（907 aa） Chain B 130–1036（907 aa） Chain C 130–1036（907 aa） Chain D 130–1036（907 aa） Chain E 130–1036（907 aa） Chain F 130–1036（907 aa） Chain G 130–1036（907 aa） Chain H 130–1036（907 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
8SWK Cryo-EM structure of NLRP3 closed hexamer Deposited 2023-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–1036（904 aa） Chain B 133–1036（904 aa） Chain C 133–1036（904 aa） Chain D 133–1036（904 aa） Chain E 133–1036（904 aa） Chain F 133–1036（904 aa）	Not recorded	7YN 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.32 Å
8SXN Structure of NLRP3 and NEK7 complex Deposited 2023-05-22	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 × 4 PDB declaration: tetrameric	Chain C 133–1036（904 aa） Chain D 133–1036（904 aa）	Not recorded	7YN 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.04 Å
8WSM NLRP3 NACHT domain in complex with compound 32 Deposited 2023-10-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 XE3 2-[[2-methyl-5-(trifluoromethyl)phenyl]amino]-~{N}-(1,4-oxazepan-4-ylsulfonyl)-1,3-oxazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M Tris pH 7.5, 1.2 M sodium citrate	Resolution 2.70 Å R-free 0.248
8ZEM Crystal Structure of NLRP3 NACHT domain in complex with NP3-1 Deposited 2024-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa）	Not recorded	A1D79 1-[5-[2,3-bis(chloranyl)phenyl]-2,3-dihydro-1~{H}-inden-4-yl]-3-[4-(2-oxidanylpropan-2-yl)thiophen-2-yl]sulfonyl-urea × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；23~25 % w/v Polyethylene glycol monomethyl ether 5,000 ;100 mM MES pH 6.3~6.7 ;200 mM Ammonium sulfate	Resolution 3.32 Å R-free 0.347
9DH3 Cryo-EM structure of NLRP3 complex with Compound C Deposited 2024-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 136–1036（901 aa） Chain B 136–1036（901 aa） Chain C 136–1036（901 aa） Chain D 136–1036（901 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4 A1A4L 2-[(4S)-5-ethyl-8-oxothieno[2',3':4,5]pyrrolo[1,2-d][1,2,4]triazin-7(8H)-yl]-N-(pyrimidin-4-yl)acetamide × 4 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.76 Å
9GU4 Crystal structure of NLRP3 in complex with inhibitor NP3-253 Deposited 2024-09-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa）	Not recorded	A1IPJ 2-[6-[[(3R)-1-ethylpiperidin-3-yl]amino]pyridazin-3-yl]-3-methyl-5-(trifluoromethyl)phenol × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；protein: well = 1: 1 well: 1.94 M Ammonium citrate pH 7.0 protein: 7 mg/ml, 1mM inhibitor co-complex	Resolution 2.70 Å R-free 0.264
9HG4 NACHT domain of NLRP3 in complex with DFV890 Deposited 2024-11-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa）	Not recorded	A1IUG 1-[azanyl-oxidanylidene-[2-(2-oxidanylpropan-2-yl)-1,3-thiazol-5-yl]-$l^{6}-sulfanylidene]-3-(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)urea × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；protein: 0.2 ul NLRP3 (131-679) at 7 mg/ml in 50mM HEPES pH 7.8, 500mM NaCl, 10% glycerol, 1mM MgCl2, 1mM TCEP, 100uM ADP, and 0.8 mM DFV890 (in DMSO) wel: 0.2 ul 1.99M NH4 3 citrate	Resolution 2.77 Å R-free 0.264
9MGY Cryo-EM structure of Human NLRP3 complex with compound 1 Deposited 2024-12-11	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–1036（1036 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 A1BLR (2M)-2-(6-{[(3R)-1-methylpiperidin-3-yl]amino}pyridazin-3-yl)-5-(trifluoromethyl)phenol × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9MIE Human NLRP3 complex with compound 2 in the closed hexamer Deposited 2024-12-12	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–1036（1036 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 A1BLP (2P)-2-(4-{[(3R)-1-methylpiperidin-3-yl]amino}-6,7-dihydro-5H-cyclopenta[d]pyridazin-1-yl)-5-(trifluoromethyl)phenol × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.93 Å
9MIG Cryo-EM structure of Human NLRP3 complex with compound 3 Deposited 2024-12-12	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–1036（1036 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 A1BLQ (2P)-2-(4-{[(3R)-1-methylpiperidin-3-yl]amino}-5,6,7,8-tetrahydrophthalazin-1-yl)-5-(trifluoromethyl)phenol × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9SFG Crystal structure of NLRP3 in complex with inhibitor NP3-742 Deposited 2025-08-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–679（549 aa）	Not recorded	A1JNK 5-methyl-~{N}-[(3~{R})-1-methylpiperidin-3-yl]-6-(2-methyl-1~{H}-pyrrolo[2,3-b]pyridin-6-yl)pyridazin-3-amine × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；protein: well = 1: 1 well: 1.94 M Ammonium citrate pH 7.0 protein: 7 mg/ml, 1mM inhibitor co-complex	Resolution 3.20 Å R-free 0.279

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NALP3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–110； UniProt 3–112 Author chain B； PDBConstruct 1–110； UniProt 3–112

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	3qf2
Deposition date deposition_date	2011-01-21
Structure title title	Crystal structure of NALP3 PYD
Keywords keywords	Six helix bundle, Apoptosis; 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	21.27 Å
Radius of gyration Rg (electron density) rg_electron	20.45 Å
Forward intensity I(0) i0	9560830.00
Molecular weight molecular_weight	22853.0 kDa
Excluded volume excluded_volume	28575 Å³
Envelope volume envelope_volume	34760 Å³
Hydration-shell volume shell_volume	15220 Å³
Envelope diameter envelope_diameter	73.8 Å
Shell Rg shell_rg	25.38 Å
Envelope Rg envelope_rg	20.79 Å
Shape Rg shape_rg	20.45 Å
Total Rg total_rg	21.22 Å
Total atoms total_atoms	1606
Residues n_residues	196
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	73.7 Å
Rg (real space) rg_real	21.43 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	9.5610e+06
I(0) uncertainty (real space) i0_real_error	1.1640e+05
Rg (reciprocal space) rg_reciprocal	21.40 Å
I(0) (reciprocal space) i0_reciprocal	9561000.0000
Solution quality estimate total_estimate	0.8112
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.5 Å
Skewness Skewness skewness	0.483
Kurtosis Kurtosis kurtosis	-0.434
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3838000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.614; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.710; Smooth: 0.989

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3qf2a_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.0 — automated matches

Domain ID domain_id	d3qf2b_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3qf2A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	3qf2B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

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8. Citations (1)

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Unit-cell length a length_a	42.032 Å
Unit-cell length b length_b	60.040 Å
Unit-cell length c length_c	51.529 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	25.610 Å
R factor r_factor	0.1859
R_work r_work	0.1833
R_free r_free	0.2350

Description description	NACHT, LRR and PYD domains-containing protein 3
Molecular weight formula_weight	12704.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1853

Crystal structure of NALP3 PYD

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

NACHT, LRR and PYD domains-containing protein 3

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 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	247

fit	/app/data/saxs_computation/qf/3qf2/3qf2.fit
pddf	/app/data/pr_computation/qf/3qf2/3qf2.pr.out
profile	/app/data/saxs_computation/qf/3qf2/3qf2.dat