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9rji

Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin-derivative KV29a (compound 5)

Method: X-RAY DIFFRACTION D_max: 125.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rji
deposition_date	2025-06-12
title	Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin-derivative KV29a (compound 5)
keywords	InhA mycobacterium tuberculosis pyridomycin derivative KV29a 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	38.27 Å
rg_electron	38.01 Å
i0	777159000.00
molecular_weight	151540.0 kDa
excluded_volume	146390 Å³
envelope_volume	260090 Å³
shell_volume	56244 Å³
envelope_diameter	129.3 Å
shell_rg	44.43 Å
envelope_rg	38.04 Å
shape_rg	38.02 Å
total_rg	38.28 Å
total_atoms	11482
n_residues	1532
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	125.5 Å
rg_real	38.27 Å
rg_real_error	1.05 Å
i0_real	7.7720e+08
i0_real_error	1.4560e+07
rg_reciprocal	38.28 Å
i0_reciprocal	777200000.0000
total_estimate	0.8912
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	39.8 Å
skewness	0.297
kurtosis	-0.573
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	107800000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.895

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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	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	12476

GSHMTGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDPSRAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL

Source

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

Entity 2 non-polymer

description	;~{N}-[(2~{Z},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-pyridine-3-carboxamide ;
formula_weight	540.6 kDa
src_method	syn
entity_count	5

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	856

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6. Citations (1)

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length_a	100.050 Å
length_b	82.140 Å
length_c	188.750 Å
angle_alpha	90.00 °
angle_beta	95.79 °
angle_gamma	90.00 °
z_pdb	24

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.766 Å
resolution_low	25.590 Å
r_factor	0.2191
r_work	0.2182
r_free	0.2355

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

Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin-derivative KV29a (compound 5)

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