SAXSdb — 9q65

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1. Structure Basics

entry_id	9q65
deposition_date	2025-08-21
title	Human prolyl endopeptidase (PREP) - complex with KT-2-75
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	53.44 Å
rg_electron	54.11 Å
i0	823725000.00
molecular_weight	243130.0 kDa
excluded_volume	305600 Å³
envelope_volume	417660 Å³
shell_volume	71041 Å³
envelope_diameter	182.7 Å
shell_rg	49.21 Å
envelope_rg	53.31 Å
shape_rg	54.11 Å
total_rg	53.92 Å
total_atoms	33813
n_residues	2118
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	172.8 Å
rg_real	54.01 Å
rg_real_error	2.10 Å
i0_real	8.2370e+08
i0_real_error	1.7180e+07
rg_reciprocal	52.94 Å
i0_reciprocal	822500000.0000
total_estimate	0.7673
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	41.7 Å
skewness	0.585
kurtosis	-0.470
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	204800000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.712; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.005

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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	B,D,F
atom_count	34283

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-[3-oxo-3-(pyrrolidin-1-yl)propyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide
formula_weight	349.8 kDa
src_method	syn
entity_count	3

Entity 3 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 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	8

Entity 5 non-polymer

description	THIOCYANATE ION
formula_weight	58.1 kDa
src_method	syn
entity_count	6

Entity 6 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	416

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6. Citations (1)

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length_a	105.522 Å
length_b	65.986 Å
length_c	159.330 Å
angle_alpha	90.00 °
angle_beta	100.47 °
angle_gamma	90.00 °
z_pdb	6

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.890 Å
resolution_low	34.600 Å
r_factor	—
r_work	0.2184
r_free	0.2954

fit	/app/data/saxs_computation/q6/9q65/9q65.fit
pddf	/app/data/pr_computation/q6/9q65/9q65.pr.out
profile	/app/data/saxs_computation/q6/9q65/9q65.dat

Human prolyl endopeptidase (PREP) - complex with KT-2-75

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