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9rzz

PYCR1 in complex with pyrrolidine-1-sulfonic acid.

Method: X-RAY DIFFRACTION D_max: 117.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rzz
deposition_date	2025-07-16
last_revision	2025-10-15
title	PYCR1 in complex with pyrrolidine-1-sulfonic acid.
keywords	;delta-1-pyrroline-5-carboxylate reductase, PYCR1, cancer, crystallographic fragment screening (XFS), molecular docking, inhibitors, proline metabolism, 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	36.92 Å
rg_electron	36.45 Å
i0	641551000.00
molecular_weight	135120.0 kDa
excluded_volume	129390 Å³
envelope_volume	233940 Å³
shell_volume	53394 Å³
envelope_diameter	121.6 Å
shell_rg	42.87 Å
envelope_rg	36.16 Å
shape_rg	36.45 Å
total_rg	36.76 Å
total_atoms	10194
n_residues	1374
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	117.5 Å
rg_real	36.81 Å
rg_real_error	0.93 Å
i0_real	6.4160e+08
i0_real_error	1.1800e+07
rg_reciprocal	36.88 Å
i0_reciprocal	641600000.0000
total_estimate	0.8937
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.2 Å
skewness	0.214
kurtosis	-0.446
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	125300000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.860

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
formula_weight	35961.4 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	11150

MHHHHHHSSGVDLGTENLYFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQEQVSPAAIKKTILDKVKLDSPAGTALSPSGHTKLLPRSLAPAGKD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	10

Entity 3 non-polymer

description	pyrrolidine-1-sulfonic acid
formula_weight	151.2 kDa
src_method	syn
entity_count	5

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	808

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6. Citations (1)

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length_a	164.549 Å
length_b	88.040 Å
length_c	116.662 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	1.700 Å
resolution_low	46.550 Å
r_factor	0.1909
r_work	0.1907
r_free	0.2149

fit	/app/data/saxs_computation/rz/9rzz/9rzz.fit
pddf	/app/data/pr_computation/rz/9rzz/9rzz.pr.out
profile	/app/data/saxs_computation/rz/9rzz/9rzz.dat

PYCR1 in complex with pyrrolidine-1-sulfonic acid.

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