SAXSdb — 9q6j

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1. Structure Basics

entry_id	9q6j
deposition_date	2025-08-22
title	Human prolyl endopeptidase (PREP) - complex with KT-2-126
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	53.43 Å
rg_electron	54.17 Å
i0	839965000.00
molecular_weight	245950.0 kDa
excluded_volume	309310 Å³
envelope_volume	421370 Å³
shell_volume	71559 Å³
envelope_diameter	187.8 Å
shell_rg	49.35 Å
envelope_rg	53.27 Å
shape_rg	54.20 Å
total_rg	53.91 Å
total_atoms	34218
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	174.9 Å
rg_real	54.00 Å
rg_real_error	1.86 Å
i0_real	8.4000e+08
i0_real_error	1.6830e+07
rg_reciprocal	52.93 Å
i0_reciprocal	838700000.0000
total_estimate	0.7634
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	42.2 Å
skewness	0.588
kurtosis	-0.454
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	176300000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.694; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.824; Smooth: 0.015

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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	36268

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	4

Entity 3 non-polymer

description	4-chloro-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-3-phenyl-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide
formula_weight	502.0 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	16

Entity 5 non-polymer

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

Entity 6 non-polymer

description	THIOCYANATE ION
formula_weight	58.1 kDa
src_method	syn
entity_count	11

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1853

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6. Citations (1)

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length_a	106.127 Å
length_b	66.936 Å
length_c	157.183 Å
angle_alpha	90.00 °
angle_beta	99.28 °
angle_gamma	90.00 °
z_pdb	6

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.750 Å
resolution_low	43.800 Å
r_factor	—
r_work	0.1642
r_free	0.2261

fit	/app/data/saxs_computation/q6/9q6j/9q6j.fit
pddf	/app/data/pr_computation/q6/9q6j/9q6j.pr.out
profile	/app/data/saxs_computation/q6/9q6j/9q6j.dat

Human prolyl endopeptidase (PREP) - complex with KT-2-126

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