SAXSdb — 9q5x

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1. Structure Basics

entry_id	9q5x
deposition_date	2025-08-21
title	Human prolyl endopeptidase (PREP) - complex with KT-2-74
keywords	inhibitor-bound, 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	51.65 Å
rg_electron	52.14 Å
i0	840393000.00
molecular_weight	245870.0 kDa
excluded_volume	309250 Å³
envelope_volume	415500 Å³
shell_volume	72081 Å³
envelope_diameter	176.5 Å
shell_rg	49.04 Å
envelope_rg	51.50 Å
shape_rg	52.14 Å
total_rg	52.02 Å
total_atoms	34222
n_residues	2123
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	165.1 Å
rg_real	52.10 Å
rg_real_error	1.64 Å
i0_real	8.4040e+08
i0_real_error	1.7090e+07
rg_reciprocal	51.25 Å
i0_reciprocal	839400000.0000
total_estimate	0.7848
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.0 Å
skewness	0.582
kurtosis	-0.434
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	238700000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.760; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.006

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

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	36948

GMLSLQYPDVYRDETAVQDYHGHKICDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNSYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESSGIAGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRQSPNYRVINIDFRDPEESKWKVLVPEHEKDVLEWIACVRSNFLVLCYLHDVKNILQLHDLTTGALLKTFPLDVGSIVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGILAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVAACANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLVKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQSNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNVDWIP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	4-chloro-1,3-dimethyl-N-(2-{[3-oxo-3-(pyrrolidin-1-yl)propyl](3-phenylpropyl)amino}ethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide
formula_weight	511.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	THIOCYANATE ION
formula_weight	58.1 kDa
src_method	syn
entity_count	8

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	14

Entity 6 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	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2322

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6. Citations (1)

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length_a	103.822 Å
length_b	66.473 Å
length_c	156.856 Å
angle_alpha	90.00 °
angle_beta	102.07 °
angle_gamma	90.00 °
z_pdb	6

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.410 Å
resolution_low	34.600 Å
r_factor	—
r_work	0.1551
r_free	0.1922

fit	/app/data/saxs_computation/q5/9q5x/9q5x.fit
pddf	/app/data/pr_computation/q5/9q5x/9q5x.pr.out
profile	/app/data/saxs_computation/q5/9q5x/9q5x.dat

Human prolyl endopeptidase (PREP) - complex with KT-2-74

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