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9rjp

Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative KV25a (compound 15)

Method: X-RAY DIFFRACTION D_max: 95.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rjp
deposition_date	2025-06-12
title	Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative KV25a (compound 15)
keywords	InhA mycobacterium tuberculosis pyridomycin complex inhibitor, OXIDOREDUCTASE; OXIDOREDUCTASE
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	29.41 Å
rg_electron	28.54 Å
i0	382406000.00
molecular_weight	104120.0 kDa
excluded_volume	100310 Å³
envelope_volume	166430 Å³
shell_volume	46064 Å³
envelope_diameter	98.3 Å
shell_rg	37.77 Å
envelope_rg	28.87 Å
shape_rg	28.55 Å
total_rg	29.10 Å
total_atoms	7881
n_residues	1041
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	95.8 Å
rg_real	29.27 Å
rg_real_error	0.73 Å
i0_real	3.8240e+08
i0_real_error	6.1630e+06
rg_reciprocal	29.33 Å
i0_reciprocal	382400000.0000
total_estimate	0.7592
solution_quality	GOOD a GOOD solution
n_peaks	5
r_peak_primary	40.8 Å
skewness	0.212
kurtosis	-0.378
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	83610000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.679; Stabil: 0.947; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Enoyl-[acyl-carrier-protein] reductase [NADH]
formula_weight	28837.1 kDa
ec_number	1.3.1.9
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8496

GSHMTGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDPSRAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL

Source

organism	Mycobacterium tuberculosis
ncbi_taxonomy_id	1773
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	;~{N}-[(5~{R},6~{S},9~{S},10~{S},11~{R})-2-butan-2-ylidene-5,11-dimethyl-10-oxidanyl-3,7,12-tris(oxidanylidene)-9-(pyridin-3-ylmethyl)-1,4-dioxa-8-azacyclododec-6-yl]-4-oxidanyl-1,2,5-thiadiazole-3-carboxamide ;
formula_weight	547.6 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	555

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6. Citations (1)

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length_a	82.120 Å
length_b	81.180 Å
length_c	95.620 Å
angle_alpha	90.00 °
angle_beta	99.89 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.145 Å
resolution_low	31.400 Å
r_factor	0.2109
r_work	0.2098
r_free	0.2316

fit	/app/data/saxs_computation/rj/9rjp/9rjp.fit
pddf	/app/data/pr_computation/rj/9rjp/9rjp.pr.out
profile	/app/data/saxs_computation/rj/9rjp/9rjp.dat

Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative KV25a (compound 15)

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