← Back to search

9s01

PYCR1 in complex with L-tartrate

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

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9s01
deposition_date	2025-07-16
last_revision	2025-10-15
title	PYCR1 in complex with L-tartrate
keywords	;delta-1-pyrroline-5-carboxylate reductase, PYCR1, cancer, crystallographic fragment screening (XFS), molecular docking, proline metabolism, OXIDOREDUCTASE ;; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	37.14 Å
rg_electron	36.50 Å
i0	318775000.00
molecular_weight	144040.0 kDa
excluded_volume	180420 Å³
envelope_volume	234740 Å³
shell_volume	53510 Å³
envelope_diameter	121.9 Å
shell_rg	42.87 Å
envelope_rg	36.18 Å
shape_rg	36.51 Å
total_rg	36.86 Å
total_atoms	10088
n_residues	1372
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	118.0 Å
rg_real	37.02 Å
rg_real_error	0.97 Å
i0_real	3.1880e+08
i0_real_error	4.8300e+06
rg_reciprocal	37.10 Å
i0_reciprocal	318800000.0000
total_estimate	0.8942
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.4 Å
skewness	0.213
kurtosis	-0.447
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	113400000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.858

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
formula_weight	36075.5 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	10910

MHHHHHHSSGVDLGTENNLYFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQEQVSPAAIKKTILDKVKLDSPAGTALSPSGHTKLLPRSLAPAGKD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	L(+)-TARTARIC ACID
formula_weight	150.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	674

▶

6. Citations (1)

▶

length_a	164.196 Å
length_b	88.109 Å
length_c	116.245 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	20

space_group	P 21 21 2
int_tables_number	18
crystal_system	orthorhombic

resolution	1.650 Å
resolution_low	37.210 Å
r_factor	0.1827
r_work	0.1825
r_free	0.2038

fit	/app/data/saxs_computation/s0/9s01/9s01.fit
pddf	/app/data/pr_computation/s0/9s01/9s01.pr.out
profile	/app/data/saxs_computation/s0/9s01/9s01.dat

PYCR1 in complex with L-tartrate

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