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9s5x

;Crystal structure of Neisseria gonorrhoeae FabI in complex with NADH and (E)-3-((2R,3S)-3-hydroxy-2-methyl-4-oxo-2,3,4,5-tetrahydro-1H-pyrido[2,3-b][1,4]diazepin-8-yl)-N-methyl-N-((3-methylbenzofuran-2-yl)methyl)acrylamide ;

Method: X-RAY DIFFRACTION D_max: 78.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s5x
deposition_date	2025-07-30
title	;Crystal structure of Neisseria gonorrhoeae FabI in complex with NADH and (E)-3-((2R,3S)-3-hydroxy-2-methyl-4-oxo-2,3,4,5-tetrahydro-1H-pyrido[2,3-b][1,4]diazepin-8-yl)-N-methyl-N-((3-methylbenzofuran-2-yl)methyl)acrylamide ;
keywords	Enoyl-[acyl-carrier-protein] reductase [NADH] Neisseria gonorrhoeae, HYDROLASE, 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	24.54 Å
rg_electron	23.74 Å
i0	104375000.00
molecular_weight	52779.0 kDa
excluded_volume	50528 Å³
envelope_volume	82814 Å³
shell_volume	28596 Å³
envelope_diameter	79.5 Å
shell_rg	31.54 Å
envelope_rg	24.09 Å
shape_rg	23.73 Å
total_rg	24.41 Å
total_atoms	3985
n_residues	515
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	78.5 Å
rg_real	24.48 Å
rg_real_error	0.46 Å
i0_real	1.0440e+08
i0_real_error	1.3830e+06
rg_reciprocal	24.50 Å
i0_reciprocal	104400000.0000
total_estimate	0.8988
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.6 Å
skewness	0.303
kurtosis	-0.401
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	18800000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.977

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Enoyl-[acyl-carrier-protein] reductase [NADH]
formula_weight	30062.1 kDa
ec_number	1.3.1.9
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4427

MHHHHHHSSGVDLGTENLYFQGFLQGKKILITGMISERSIAYGIAKACREQGAELAFTYVVDKLEERVRKMAAELDSELVFRCDVASDDEINQVFADLGKHWDGLDGLVHSIGFAPKEALSGDFLDSISREAFNTAHEISAYSLPALAKAARPMMRGRNSAIVALSYLGAVRAIPNYNVMGMAKASLEAGIRFTAACLGKEGIRCNGISAGPIKTLAASGIADFGKLLGHVAAHNPLRRNVTIEEVGNTAAFLLSDLSSGITGEITYVDGGYSINALSTEG

Source

organism	Neisseria gonorrhoeae
ncbi_taxonomy_id	485
host_organism	Escherichia coli

Entity 2 non-polymer

description	;(~{E})-~{N}-methyl-~{N}-[(3-methyl-1-benzofuran-2-yl)methyl]-3-[(2~{R},3~{S})-2-methyl-3-oxidanyl-4-oxidanylidene-1,2,3,5-tetrahydropyrido[2,3-b][1,4]diazepin-8-yl]prop-2-enamide ;
formula_weight	420.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	412

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6. Citations (1)

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length_a	91.260 Å
length_b	91.260 Å
length_c	241.060 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 61 2 2
int_tables_number	178
crystal_system	—

resolution	1.340 Å
resolution_low	75.210 Å
r_factor	0.1680
r_work	0.1666
r_free	0.1964

fit	/app/data/saxs_computation/s5/9s5x/9s5x.fit
pddf	/app/data/pr_computation/s5/9s5x/9s5x.pr.out
profile	/app/data/saxs_computation/s5/9s5x/9s5x.dat

;Crystal structure of Neisseria gonorrhoeae FabI in complex with NADH and (E)-3-((2R,3S)-3-hydroxy-2-methyl-4-oxo-2,3,4,5-tetrahydro-1H-pyrido[2,3-b][1,4]diazepin-8-yl)-N-methyl-N-((3-methylbenzofuran-2-yl)methyl)acrylamide ;

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