SAXSdb — 9q64

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1. Structure Basics

entry_id	9q64
deposition_date	2025-08-21
title	Human prolyl endopeptidase (PREP) - complex with KT-2-59
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	44.67 Å
rg_electron	44.37 Å
i0	1664210000.00
molecular_weight	227040.0 kDa
excluded_volume	220870 Å³
envelope_volume	399010 Å³
shell_volume	74296 Å³
envelope_diameter	144.1 Å
shell_rg	49.85 Å
envelope_rg	43.59 Å
shape_rg	44.38 Å
total_rg	44.52 Å
total_atoms	17209
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	144.1 Å
rg_real	44.52 Å
rg_real_error	1.37 Å
i0_real	1.6640e+09
i0_real_error	3.0220e+07
rg_reciprocal	44.67 Å
i0_reciprocal	1664000000.0000
total_estimate	0.8994
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	45.3 Å
skewness	0.137
kurtosis	-0.709
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	261000000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.941

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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	18610

GMLSLQYPDVYRDETAVQDYHGHKICDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNSYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESSGIAGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRQSPNYRVINIDFRDPEESKWKVLVPEHEKDVLEWIACVRSNFLVLCYLHDVKNILQLHDLTTGALLKTFPLDVGSIVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGILAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVAACANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLVKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQSNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNVDWIP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,3-dimethyl-N-[(pyridin-3-yl)methyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide
formula_weight	315.8 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	13

Entity 4 non-polymer

description	THIOCYANATE ION
formula_weight	58.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	3

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	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1372

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6. Citations (1)

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length_a	105.888 Å
length_b	67.026 Å
length_c	157.386 Å
angle_alpha	90.00 °
angle_beta	99.41 °
angle_gamma	90.00 °
z_pdb	6

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.940 Å
resolution_low	34.100 Å
r_factor	0.1593
r_work	0.1555
r_free	0.2331

fit	/app/data/saxs_computation/q6/9q64/9q64.fit
pddf	/app/data/pr_computation/q6/9q64/9q64.pr.out
profile	/app/data/saxs_computation/q6/9q64/9q64.dat

Human prolyl endopeptidase (PREP) - complex with KT-2-59

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