SAXSdb — 9q5y

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1. Structure Basics

entry_id	9q5y
deposition_date	2025-08-21
title	Human prolyl endopeptidase (PREP) - complex with YX45
keywords	apo form, peptide cleavage, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE 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	53.33 Å
rg_electron	54.04 Å
i0	828382000.00
molecular_weight	244730.0 kDa
excluded_volume	307990 Å³
envelope_volume	420600 Å³
shell_volume	71548 Å³
envelope_diameter	187.2 Å
shell_rg	49.41 Å
envelope_rg	53.15 Å
shape_rg	54.05 Å
total_rg	53.82 Å
total_atoms	34087
n_residues	2121
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	173.7 Å
rg_real	53.89 Å
rg_real_error	2.22 Å
i0_real	8.2840e+08
i0_real_error	1.7210e+07
rg_reciprocal	52.84 Å
i0_reciprocal	827100000.0000
total_estimate	0.5509
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	46.3 Å
skewness	0.590
kurtosis	-0.447
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	214700000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.700; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.860; Smooth: 0.012

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Prolyl endopeptidase
formula_weight	80851.4 kDa
ec_number	3.4.21.26
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	36295

GMLSLQYPDVYRDETAVQDYHGHKICDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNSYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESSGIAGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRQSPNYRVINIDFRDPEESKWKVLVPEHEKDVLEWIACVRSNFLVLCYLHDVKNILQLHDLTTGALLKTFPLDVGSIVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGILAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVAACANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLVKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQSNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNVDWIP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	282.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	2-[4-chloro-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-1-(pyrrolidin-1-yl)ethan-1-one
formula_weight	368.9 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	20

Entity 5 non-polymer

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

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1975

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6. Citations (1)

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length_a	106.220 Å
length_b	66.877 Å
length_c	156.909 Å
angle_alpha	90.00 °
angle_beta	99.29 °
angle_gamma	90.00 °
z_pdb	6

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.490 Å
resolution_low	34.940 Å
r_factor	—
r_work	0.1634
r_free	0.2065

fit	/app/data/saxs_computation/q5/9q5y/9q5y.fit
pddf	/app/data/pr_computation/q5/9q5y/9q5y.pr.out
profile	/app/data/saxs_computation/q5/9q5y/9q5y.dat

Human prolyl endopeptidase (PREP) - complex with YX45

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