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9rjm

Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative EP196 (compound 13)

Method: X-RAY DIFFRACTION D_max: 122.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rjm
deposition_date	2025-06-12
title	Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative EP196 (compound 13)
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	39.15 Å
rg_electron	38.61 Å
i0	800850000.00
molecular_weight	153610.0 kDa
excluded_volume	148240 Å³
envelope_volume	276800 Å³
shell_volume	58447 Å³
envelope_diameter	127.8 Å
shell_rg	45.74 Å
envelope_rg	37.83 Å
shape_rg	38.60 Å
total_rg	38.91 Å
total_atoms	11631
n_residues	1548
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	122.3 Å
rg_real	38.93 Å
rg_real_error	0.71 Å
i0_real	8.0080e+08
i0_real_error	1.1470e+07
rg_reciprocal	39.07 Å
i0_reciprocal	801000000.0000
total_estimate	0.9037
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	52.0 Å
skewness	0.094
kurtosis	-0.607
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	62750000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.909

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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	12576

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-fluoranyl-3-oxidanyl-pyridine-2-carboxamide ;
formula_weight	558.6 kDa
src_method	syn
entity_count	6

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	854

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6. Citations (1)

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length_a	100.040 Å
length_b	82.580 Å
length_c	188.610 Å
angle_alpha	90.00 °
angle_beta	95.94 °
angle_gamma	90.00 °
z_pdb	24

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.986 Å
resolution_low	187.600 Å
r_factor	0.2009
r_work	0.1995
r_free	0.2267

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

Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative EP196 (compound 13)

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