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9r9d

;Recombinant human butyrylcholinesterase in complex with N-(2-methoxyethyl)-N-{[1-(prop-2-yn-1-yl)pyrrolidin-3-yl]methyl}naphthalene-2-carboxamide ;

Method: X-RAY DIFFRACTION D_max: 77.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r9d
deposition_date	2025-05-20
last_revision	2025-08-13
title	;Recombinant human butyrylcholinesterase in complex with N-(2-methoxyethyl)-N-{[1-(prop-2-yn-1-yl)pyrrolidin-3-yl]methyl}naphthalene-2-carboxamide ;
keywords	Butyrylcholinesterase, inhibitor, complex, HYDROLASE; 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	24.10 Å
rg_electron	23.02 Å
i0	118073000.00
molecular_weight	58152.0 kDa
excluded_volume	56654 Å³
envelope_volume	89616 Å³
shell_volume	31081 Å³
envelope_diameter	79.9 Å
shell_rg	31.49 Å
envelope_rg	23.45 Å
shape_rg	22.97 Å
total_rg	23.78 Å
total_atoms	4408
n_residues	526
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	77.0 Å
rg_real	23.95 Å
rg_real_error	0.43 Å
i0_real	1.1810e+08
i0_real_error	1.5380e+06
rg_reciprocal	23.98 Å
i0_reciprocal	118100000.0000
total_estimate	0.7087
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	30.1 Å
skewness	0.181
kurtosis	-0.408
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	27160000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 0.203; Positv: 1.000; Valcen: 0.995; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Cholinesterase
formula_weight	59713.5 kDa
ec_number	3.1.1.8
mutation	;N17Q, N455Q, N481Q, N486Q mutations compared to mature wild type sequence to avoid too much N-glycozylation. Numeration on the maturated enzyme (devoid of the signal peptide) ;
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4660

EDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 2 branched

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

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	3

Entity 4 non-polymer

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

Entity 5 non-polymer

description	~{N}-(2-methoxyethyl)-~{N}-[[(3~{R})-1-prop-2-ynylpyrrolidin-3-yl]methyl]naphthalene-2-carboxamide
formula_weight	350.5 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	210

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6. Citations (1)

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length_a	153.408 Å
length_b	153.408 Å
length_c	127.609 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 4 2 2
int_tables_number	97
crystal_system	tetragonal

resolution	2.160 Å
resolution_low	41.320 Å
r_factor	0.1791
r_work	0.1774
r_free	0.2138

fit	/app/data/saxs_computation/r9/9r9d/9r9d.fit
pddf	/app/data/pr_computation/r9/9r9d/9r9d.pr.out
profile	/app/data/saxs_computation/r9/9r9d/9r9d.dat