SAXSdb — 9xzz

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1. Structure Basics

entry_id	9xzz
deposition_date	2025-08-28
title	Human prolyl endopeptidase (PREP) - complex with KYP2047
keywords	inhibitor-bound, peptide cleavage, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex, HYDROLASE-INHIBITOR complex; 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	51.52 Å
rg_electron	52.02 Å
i0	845044000.00
molecular_weight	244530.0 kDa
excluded_volume	306800 Å³
envelope_volume	412660 Å³
shell_volume	71698 Å³
envelope_diameter	174.6 Å
shell_rg	48.92 Å
envelope_rg	51.39 Å
shape_rg	52.01 Å
total_rg	51.95 Å
total_atoms	34051
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	164.3 Å
rg_real	51.97 Å
rg_real_error	2.03 Å
i0_real	8.4500e+08
i0_real_error	1.7210e+07
rg_reciprocal	51.12 Å
i0_reciprocal	844100000.0000
total_estimate	0.7766
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	42.4 Å
skewness	0.578
kurtosis	-0.442
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	242500000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.799; Smooth: 0.005

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	36305

GMLSLQYPDVYRDETAVQDYHGHKICDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNSYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESSGIAGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRQSPNYRVINIDFRDPEESKWKVLVPEHEKDVLEWIACVRSNFLVLCYLHDVKNILQLHDLTTGALLKTFPLDVGSIVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGILAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVAACANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLVKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQSNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNVDWIP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	(2S)-1-[1-(4-phenylbutanoyl)-L-prolyl]pyrrolidine-2-carbonitrile
formula_weight	341.4 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	15

Entity 4 non-polymer

description	THIOCYANATE ION
formula_weight	58.1 kDa
src_method	syn
entity_count	6

Entity 5 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 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2051

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6. Citations (1)

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length_a	103.582 Å
length_b	66.227 Å
length_c	156.431 Å
angle_alpha	90.00 °
angle_beta	102.19 °
angle_gamma	90.00 °
z_pdb	6

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.580 Å
resolution_low	34.500 Å
r_factor	—
r_work	0.1499
r_free	0.2001

fit	/app/data/saxs_computation/xz/9xzz/9xzz.fit
pddf	/app/data/pr_computation/xz/9xzz/9xzz.pr.out
profile	/app/data/saxs_computation/xz/9xzz/9xzz.dat

Human prolyl endopeptidase (PREP) - complex with KYP2047

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