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9sfg

Crystal structure of NLRP3 in complex with inhibitor NP3-742

Method: X-RAY DIFFRACTION D_max: 82.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sfg
deposition_date	2025-08-19
title	Crystal structure of NLRP3 in complex with inhibitor NP3-742
keywords	NLRP3, Inhibitor, IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	24.04 Å
rg_electron	23.06 Å
i0	94880400.00
molecular_weight	51855.0 kDa
excluded_volume	50542 Å³
envelope_volume	83112 Å³
shell_volume	29339 Å³
envelope_diameter	86.0 Å
shell_rg	30.79 Å
envelope_rg	23.35 Å
shape_rg	23.04 Å
total_rg	23.75 Å
total_atoms	3926
n_residues	488
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	82.9 Å
rg_real	23.93 Å
rg_real_error	0.60 Å
i0_real	9.4880e+07
i0_real_error	1.3110e+06
rg_reciprocal	23.96 Å
i0_reciprocal	94880000.0000
total_estimate	0.7852
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	75.1 Å
skewness	0.252
kurtosis	-0.359
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	29510000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	NACHT, LRR and PYD domains-containing protein 3
formula_weight	64156.3 kDa
ec_number	3.6.4.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3947

GKMKKDYRKKYRKYVRSRFQCIEDRNARLGESVSLNKRYTRLRLIKEHRSQQEREQELLAIGKTKTCESPVSPIKMELLFDPDDEHSEPVHTVVFQGAAGIGKTILARKMMLDWASGTLYQDRFDYLFYIHCREVSLVTQRSLGDLIMSCCPDPNPPIHKIVRKPSRILFLMDGFDELQGAFDEHIGPLCTDWQKAERGDILLSSLIRKKLLPEASLLITTRPVALEKLQHLLDHPRHVEILGFSEAKRKEYFFKYFSDEAQARAAFSLIQENEVLFTMCFIPLVCWIVCTGLKQQMESGKSLAQTSKTTTAVYVFFLSSLLQPRGGSQEHGLCAHLWGLCSLAADGIWNQKILFEESDLRNHGLQKADVSAFLRMNLFQKEVDCEKFYSFIHMTFQEFFAAMYYLLEEEKEGRTNVPGSRLKLPSRDVTVLLENYGKFEKGYLIFVVRFLFGLVNQERTSYLEKKLSCKISQQIRLELLKWIEVKAKAKKLQIQPSQLELFYCLYEMQEEDFVQRAMDYFPKIEINLSTRMDHMVSSFCIENCHRVESL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	5-methyl-~{N}-[(3~{R})-1-methylpiperidin-3-yl]-6-(2-methyl-1~{H}-pyrrolo[2,3-b]pyridin-6-yl)pyridazin-3-amine
formula_weight	336.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	21

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6. Citations (1)

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length_a	96.150 Å
length_b	96.150 Å
length_c	260.655 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 61 2 2
int_tables_number	178
crystal_system	hexagonal

resolution	3.200 Å
resolution_low	48.070 Å
r_factor	0.2143
r_work	0.2112
r_free	0.2789

fit	/app/data/saxs_computation/sf/9sfg/9sfg.fit
pddf	/app/data/pr_computation/sf/9sfg/9sfg.pr.out
profile	/app/data/saxs_computation/sf/9sfg/9sfg.dat

Crystal structure of NLRP3 in complex with inhibitor NP3-742

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction