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9si4

Structure of human neutrophil elastase in complex with a 5,8-dihydro[1,2,4]triazolo[4,3-a]pyrimidin-3(2H)-one inhibitor

Method: X-RAY DIFFRACTION D_max: 54.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9si4
deposition_date	2025-08-28
title	Structure of human neutrophil elastase in complex with a 5,8-dihydro[1,2,4]triazolo[4,3-a]pyrimidin-3(2H)-one inhibitor
keywords	Trypsin Family Fold, Protease, Hydrolase, Hydrolase-Inhibitor Complex; HYDROLASE
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	17.41 Å
rg_electron	16.32 Å
i0	21703700.00
molecular_weight	23176.0 kDa
excluded_volume	22082 Å³
envelope_volume	34835 Å³
shell_volume	17386 Å³
envelope_diameter	53.9 Å
shell_rg	22.92 Å
envelope_rg	16.70 Å
shape_rg	16.32 Å
total_rg	17.08 Å
total_atoms	1751
n_residues	218
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	54.0 Å
rg_real	17.29 Å
rg_real_error	0.20 Å
i0_real	2.1700e+07
i0_real_error	2.1820e+05
rg_reciprocal	17.30 Å
i0_reciprocal	21700000.0000
total_estimate	0.8961
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.3 Å
skewness	0.143
kurtosis	-0.439
angular_range	— – 0.4550 Å⁻¹
current_alpha	0.0000
highest_alpha	7224000.0000
n_real_points	76
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.970

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Neutrophil elastase
formula_weight	23319.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1908

IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ

Entity 2 branched

description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	367.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	alpha-L-fucopyranose
formula_weight	164.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	;methyl (5~{R})-5-[4-cyano-2-[2-(trimethyl-$l^{4}-azanyl)ethyl]phenyl]-7-methyl-3-oxidanylidene-8-[3-(trifluoromethyl)phenyl]-2,5-dihydro-[1,2,4]triazolo[4,3-a]pyrimidine-6-carboxylate ;
formula_weight	541.5 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	141

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6. Citations (1)

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length_a	73.160 Å
length_b	73.160 Å
length_c	70.150 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 63
int_tables_number	173
crystal_system	—

resolution	1.140 Å
resolution_low	36.610 Å
r_factor	0.1351
r_work	0.1340
r_free	0.1549

fit	/app/data/saxs_computation/si/9si4/9si4.fit
pddf	/app/data/pr_computation/si/9si4/9si4.pr.out
profile	/app/data/saxs_computation/si/9si4/9si4.dat