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9u8m

Drosophila melanogaster Nicotinamidase in Complex with Inhibitor CN2

Method: X-RAY DIFFRACTION D_max: 79.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u8m
deposition_date	2025-03-26
title	Drosophila melanogaster Nicotinamidase in Complex with Inhibitor CN2
keywords	Nicotinamide, Nicotinic acid, Nicotinamide adenine dinucleotide, 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	23.57 Å
rg_electron	22.62 Å
i0	24324600.00
molecular_weight	37126.0 kDa
excluded_volume	46138 Å³
envelope_volume	54216 Å³
shell_volume	21192 Å³
envelope_diameter	83.5 Å
shell_rg	28.46 Å
envelope_rg	22.81 Å
shape_rg	22.48 Å
total_rg	23.79 Å
total_atoms	5113
n_residues	327
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	79.3 Å
rg_real	23.71 Å
rg_real_error	0.67 Å
i0_real	2.4320e+07
i0_real_error	3.3100e+05
rg_reciprocal	23.68 Å
i0_reciprocal	24320000.0000
total_estimate	0.7786
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	24.8 Å
skewness	0.496
kurtosis	-0.294
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	4107000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.750; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.871; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	nicotinamidase
formula_weight	40164.1 kDa
ec_number	3.5.1.19
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5263

MDSPTPPIVIEDSNGSAMDACFTAFDKDSDDRLSLAEFSIICRALFRNDKGHIYDVPPERLEQIFAVFDTNGDGFIDREEFKFCWNQWIKTIVRPVNAFLIVDVQNDFISGSLDISNCSAQQQGHEILEPINKLLDTVDFDAVFYSLDWHPSDHVSFIDNVKMRPMDESSALDSDSAKVFDTVIFAGPPPMKQRLWPRHCVQDSWGAELHKDLKVVDHGIKVYKGTNPEVDSYSVFWDNKKLSDTTLNAQLKMKGATDIYVCGLAYDVCVGATAVDALSAGYRTILIDDCCRGTDVHDIEHTKEKVNTSDGVIVHTNQVKAMAEGRDRRPELGYKLAMELKSPDSVLSQRNGFRPSY

Source

organism	Drosophila melanogaster
common_name	fruit fly
ncbi_taxonomy_id	7227
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	[3-(phenylmethyl)imidazol-4-yl]methanimine
formula_weight	185.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	FE (II) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	150

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6. Citations (1)

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length_a	74.863 Å
length_b	70.410 Å
length_c	76.524 Å
angle_alpha	90.00 °
angle_beta	94.46 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.758 Å
resolution_low	50.000 Å
r_factor	0.1999
r_work	0.1983
r_free	0.2294

fit	/app/data/saxs_computation/u8/9u8m/9u8m.fit
pddf	/app/data/pr_computation/u8/9u8m/9u8m.pr.out
profile	/app/data/saxs_computation/u8/9u8m/9u8m.dat