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9rly

Leishmania major N-myristoyltransferase in complex with azetidinopyrimidine inhibitor IMP-929

Method: X-RAY DIFFRACTION D_max: 76.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rly
deposition_date	2025-06-17
last_revision	2026-05-27
title	Leishmania major N-myristoyltransferase in complex with azetidinopyrimidine inhibitor IMP-929
keywords	myristoylation, azetidinopyrimidine, Leishmania, inhibitor, TRANSFERASE; TRANSFERASE
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	23.08 Å
rg_electron	22.04 Å
i0	73372600.00
molecular_weight	45510.0 kDa
excluded_volume	44360 Å³
envelope_volume	70571 Å³
shell_volume	26374 Å³
envelope_diameter	78.8 Å
shell_rg	29.44 Å
envelope_rg	22.44 Å
shape_rg	22.00 Å
total_rg	22.74 Å
total_atoms	3451
n_residues	411
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	76.4 Å
rg_real	22.98 Å
rg_real_error	0.41 Å
i0_real	7.3370e+07
i0_real_error	9.8950e+05
rg_reciprocal	23.00 Å
i0_reciprocal	73370000.0000
total_estimate	0.8850
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.2 Å
skewness	0.221
kurtosis	-0.394
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0000
highest_alpha	11010000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.973

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Glycylpeptide N-tetradecanoyltransferase
formula_weight	48195.8 kDa
ec_number	2.3.1.97
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4252

NPSNSDAAHAFWSTQPVPQTEDETEKIVFAGPMDEPKTVADIPEEPYPIASTFEWWTPNMEAADDIHAIYELLRDNYVEDDDSMFRFNYSEEFLQWALCPPNYIPDWHVAVRRKADKKLLAFIAGVPVTLRMGTPKYMKVKAQEKGEGEEAAKYDEPRHICEINFLCVHKQLREKRLAPILIKEATRRVNRTNVWQAVYTAGVLLPTPYASGQYFHRSLNPEKLVEIRFSGIPAQYQKFQNPMAMLKRNYQLPSAPKNSGLREMKPSDVPQVRRILMNYLDSFDVGPVFSDAEISHYLLPRDGVVFTYVVENDKKVTDFFSFYRIPSTVIGNSNYNLLNAAYVHYYAATSIPLHQLILDLLIVAHSRGFDVCNMVEILDNRSFVEQLKFGAGDGHLRYYFYNWAYPKIKPSQVALVML

Source

organism	Leishmania major
ncbi_taxonomy_id	5664
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	TETRADECANOYL-COA
formula_weight	977.9 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1-[5-chloranyl-2-(4-methyl-1,4-diazepan-1-yl)pyrimidin-4-yl]-~{N}-(isoquinolin-4-ylmethyl)azetidine-3-carboxamide
formula_weight	466.0 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	561

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6. Citations (1)

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length_a	47.590 Å
length_b	91.471 Å
length_c	52.887 Å
angle_alpha	90.00 °
angle_beta	111.83 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.360 Å
resolution_low	49.095 Å
r_factor	—
r_work	0.1687
r_free	0.2040

fit	/app/data/saxs_computation/rl/9rly/9rly.fit
pddf	/app/data/pr_computation/rl/9rly/9rly.pr.out
profile	/app/data/saxs_computation/rl/9rly/9rly.dat