SAXSdb — 9xyk

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1. Structure Basics

entry_id	9xyk
deposition_date	2025-08-26
title	Human prolyl endopeptidase (PREP) - complex with JP-7-1-7
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	44.33 Å
rg_electron	43.79 Å
i0	859890000.00
molecular_weight	247570.0 kDa
excluded_volume	311160 Å³
envelope_volume	396750 Å³
shell_volume	73840 Å³
envelope_diameter	143.9 Å
shell_rg	50.15 Å
envelope_rg	43.14 Å
shape_rg	43.80 Å
total_rg	44.03 Å
total_atoms	34433
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	44.20 Å
rg_real_error	1.02 Å
i0_real	8.5990e+08
i0_real_error	1.5290e+07
rg_reciprocal	44.33 Å
i0_reciprocal	860000000.0000
total_estimate	0.9001
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	48.0 Å
skewness	0.176
kurtosis	-0.660
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	271900000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.951

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

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	C,A,B
atom_count	36320

GMLSLQYPDVYRDETAVQDYHGHKICDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNSYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESSGIAGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRQSPNYRVINIDFRDPEESKWKVLVPEHEKDVLEWIACVRSNFLVLCYLHDVKNILQLHDLTTGALLKTFPLDVGSIVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGILAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVAACANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLVKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQSNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNVDWIP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	THIOCYANATE ION
formula_weight	58.1 kDa
src_method	syn
entity_count	18

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	9

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	25

Entity 5 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	5

Entity 6 non-polymer

description	4-chloro-1-(2-cyclohexylethyl)-3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide
formula_weight	432.0 kDa
src_method	syn
entity_count	3

Entity 7 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 8 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1638

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6. Citations (1)

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length_a	103.543 Å
length_b	66.302 Å
length_c	156.244 Å
angle_alpha	90.00 °
angle_beta	102.10 °
angle_gamma	90.00 °
z_pdb	6

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.730 Å
resolution_low	34.500 Å
r_factor	—
r_work	0.1891
r_free	0.2554

fit	/app/data/saxs_computation/xy/9xyk/9xyk.fit
pddf	/app/data/pr_computation/xy/9xyk/9xyk.pr.out
profile	/app/data/saxs_computation/xy/9xyk/9xyk.dat

Human prolyl endopeptidase (PREP) - complex with JP-7-1-7

SAXS Profile

P(r) Distribution