← Back to search

9qdk

Trypanosoma brucei PTR1 in complex with fragment L330 and compound F46

Method: X-RAY DIFFRACTION D_max: 92.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qdk
deposition_date	2025-03-06
last_revision	2026-03-18
title	Trypanosoma brucei PTR1 in complex with fragment L330 and compound F46
keywords	Trypanosoma brucei, pteridine reductase, PTR1, TbPTR1, fragment based drug design, NADPH, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	29.29 Å
rg_electron	28.08 Å
i0	195089000.00
molecular_weight	108570.0 kDa
excluded_volume	134750 Å³
envelope_volume	153040 Å³
shell_volume	43598 Å³
envelope_diameter	97.2 Å
shell_rg	37.04 Å
envelope_rg	28.20 Å
shape_rg	28.09 Å
total_rg	28.76 Å
total_atoms	7595
n_residues	985
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	92.2 Å
rg_real	29.15 Å
rg_real_error	0.50 Å
i0_real	1.9510e+08
i0_real_error	2.7420e+06
rg_reciprocal	29.21 Å
i0_reciprocal	195100000.0000
total_estimate	0.8961
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.6 Å
skewness	0.192
kurtosis	-0.386
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	51470000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.963

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	Pteridine reductase
formula_weight	30669.8 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8336

MGSSHHHHHHSSGLVPRGSHMEAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGDHEDNSNGKTVETQVAELIGTNAIAPFLLTMSFAQRQKGTNPNCTSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA

Source

organism	Trypanosoma brucei brucei
ncbi_taxonomy_id	5702
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
formula_weight	745.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	2-amino-3H,4H,7H-pyrrolo[2,3-d]pyrimidin-4-one
formula_weight	150.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	1-(3,4-dichlorobenzyl)-1H-benzimidazol-2-amine
formula_weight	292.2 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	627

▶

6. Citations (1)

▶

length_a	74.505 Å
length_b	89.298 Å
length_c	82.629 Å
angle_alpha	90.00 °
angle_beta	115.65 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.900 Å
resolution_low	41.740 Å
r_factor	0.1730
r_work	0.1706
r_free	0.2167

fit	/app/data/saxs_computation/qd/9qdk/9qdk.fit
pddf	/app/data/pr_computation/qd/9qdk/9qdk.pr.out
profile	/app/data/saxs_computation/qd/9qdk/9qdk.dat