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9q45

;Quaternary complex of PYCR1 with the allosteric inhibitor 1-benzyl-1H-1,3-benzodiazole-2-sulfonic acid in a remote site and NADH and (S)-tetrahydrofuran-2-carboxylic acid in the active site ;

Method: X-RAY DIFFRACTION D_max: 118.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q45
deposition_date	2025-08-19
title	;Quaternary complex of PYCR1 with the allosteric inhibitor 1-benzyl-1H-1,3-benzodiazole-2-sulfonic acid in a remote site and NADH and (S)-tetrahydrofuran-2-carboxylic acid in the active site ;
keywords	AMINO-ACID BIOSYNTHESIS, OXIDOREDUCTASE, PROLINE BIOSYNTHESIS, INHIBITOR, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex; OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
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	36.56 Å
rg_electron	36.11 Å
i0	640695000.00
molecular_weight	134290.0 kDa
excluded_volume	128190 Å³
envelope_volume	229040 Å³
shell_volume	52665 Å³
envelope_diameter	120.7 Å
shell_rg	42.62 Å
envelope_rg	35.90 Å
shape_rg	36.11 Å
total_rg	36.41 Å
total_atoms	10120
n_residues	1387
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	118.0 Å
rg_real	36.45 Å
rg_real_error	0.79 Å
i0_real	6.4070e+08
i0_real_error	9.8190e+06
rg_reciprocal	36.52 Å
i0_reciprocal	640700000.0000
total_estimate	0.8931
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.4 Å
skewness	0.209
kurtosis	-0.446
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	173600000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.916

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Pyrroline-5-carboxylate reductase 1, mitochondrial
formula_weight	33532.6 kDa
ec_number	1.5.1.2
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	11084

MHHHHHHSSGVDLGTENLYFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQEQVSPAAIKKTILDKVKLDS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	TETRAHYDROFURAN-2-CARBOXYLIC ACID
formula_weight	116.1 kDa
src_method	syn
entity_count	5

Entity 3 non-polymer

description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
formula_weight	665.4 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	1-benzyl-1H-1,3-benzimidazole-2-sulfonic acid
formula_weight	288.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

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

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	839

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6. Citations (1)

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length_a	111.040 Å
length_b	179.738 Å
length_c	88.217 Å
angle_alpha	90.00 °
angle_beta	106.77 °
angle_gamma	90.00 °
z_pdb	20

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.790 Å
resolution_low	55.570 Å
r_factor	0.1981
r_work	0.1966
r_free	0.2253

fit	/app/data/saxs_computation/q4/9q45/9q45.fit
pddf	/app/data/pr_computation/q4/9q45/9q45.pr.out
profile	/app/data/saxs_computation/q4/9q45/9q45.dat