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9vp7

Glucose-6-phosphate dehydrogenase from Leishmania donovani in complex with pseudo substrate

Method: X-RAY DIFFRACTION D_max: 115.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vp7
deposition_date	2025-07-02
last_revision	2025-11-05
title	Glucose-6-phosphate dehydrogenase from Leishmania donovani in complex with pseudo substrate
keywords	Glucose-6-phosphate dehydrogenase, Rosman fold, Complex form, pseudo substrate, 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	35.96 Å
rg_electron	35.10 Å
i0	201917000.00
molecular_weight	115150.0 kDa
excluded_volume	144360 Å³
envelope_volume	193820 Å³
shell_volume	45614 Å³
envelope_diameter	123.4 Å
shell_rg	42.23 Å
envelope_rg	34.30 Å
shape_rg	35.11 Å
total_rg	35.59 Å
total_atoms	8116
n_residues	1049
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	115.0 Å
rg_real	35.86 Å
rg_real_error	0.80 Å
i0_real	2.0190e+08
i0_real_error	3.5010e+06
rg_reciprocal	35.92 Å
i0_reciprocal	201900000.0000
total_estimate	0.9065
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	44.4 Å
skewness	0.200
kurtosis	-0.534
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	25300000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.947

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Glucose-6-phosphate 1-dehydrogenase
formula_weight	66933.8 kDa
ec_number	1.1.1.49
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8840

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSEEQSHADQDAYVADVDGILDVLRAQVLERKPDDIFQFISKSALSLQKDRGAESCDRINCKVKDEQKSRALTIIVFGASGDLAKKKTFPALFDLYCGGLLPPEVNIIGYARTKVDDVEKWKHETLMKYFSNLSERGCHAEDFLKHISYFCGAYDSVDDFKRLDAVIREKENAFKGPEKGGNRLFYLALPPSVFASVCESIHKGAMPQEVGGWVRVIIEKPFGRDTKSSAELSQALEPFFDESQLYRIDHYLGKEMVQNIITTRFANRIFSAVWNASNIACVQITFKETIGTEGRGGYFDSIGIIRDVMQNHLTQILALLAMEKPRSLDAECIRDEKVSVLKCIEPITKENCVLGQYTASADGSIPGYLEDVTVPEGSTCPTFAVMRLNINNDRWAGVPFILKAGKAVEQKYVAIRIQFRDEVHPYGEATQRNELVIRAQPSEAMYVKITTKVPGLSGDLRQTHQTELDLTYHTRYDVRLPDAYESLINDALLGNSTNFVRKDELDVAWRIFTPLLHQIDSGEIKPIPYQAGTRGPKEADEFIANNGFKHQKGYHWLPSNKL

Source

organism	Leishmania donovani
ncbi_taxonomy_id	5661
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose
formula_weight	259.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	724

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6. Citations (1)

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length_a	191.840 Å
length_b	97.685 Å
length_c	70.449 Å
angle_alpha	90.00 °
angle_beta	94.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.250 Å
resolution_low	30.195 Å
r_factor	—
r_work	0.2196
r_free	0.2863

fit	/app/data/saxs_computation/vp/9vp7/9vp7.fit
pddf	/app/data/pr_computation/vp/9vp7/9vp7.pr.out
profile	/app/data/saxs_computation/vp/9vp7/9vp7.dat