← Back to search

9rjk

Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative KV41a (compound 11)

Method: X-RAY DIFFRACTION D_max: 92.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rjk
deposition_date	2025-06-12
title	Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative KV41a (compound 11)
keywords	InhA mycobacterium tuberculosis pyridomycin derivative complex inhibitor, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	29.20 Å
rg_electron	28.34 Å
i0	365786000.00
molecular_weight	102180.0 kDa
excluded_volume	98664 Å³
envelope_volume	162220 Å³
shell_volume	45328 Å³
envelope_diameter	100.1 Å
shell_rg	37.45 Å
envelope_rg	28.64 Å
shape_rg	28.35 Å
total_rg	28.91 Å
total_atoms	7739
n_residues	1020
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

▼

3. P(r) Analysis (GNOM)

dmax	92.8 Å
rg_real	29.07 Å
rg_real_error	0.51 Å
i0_real	3.6580e+08
i0_real_error	5.3310e+06
rg_reciprocal	29.13 Å
i0_reciprocal	365800000.0000
total_estimate	0.8917
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.1 Å
skewness	0.221
kurtosis	-0.357
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	71600000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.966

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

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	8671

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]-3-fluoranyl-2-oxidanyl-benzamide ;
formula_weight	557.6 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	816

▶

6. Citations (1)

▶

length_a	82.070 Å
length_b	81.350 Å
length_c	95.480 Å
angle_alpha	90.00 °
angle_beta	99.41 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.658 Å
resolution_low	94.190 Å
r_factor	0.1864
r_work	0.1855
r_free	0.2050

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

Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative KV41a (compound 11)

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