SAXSdb — 9xyl

▼

1. Structure Basics

entry_id	9xyl
deposition_date	2025-08-26
title	Human prolyl endopeptidase (PREP) - complex with S17092
keywords	inhibitor-bound, peptide cleavage, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	72.91 Å
rg_electron	73.73 Å
i0	3168360000.00
molecular_weight	486410.0 kDa
excluded_volume	612120 Å³
envelope_volume	881170 Å³
shell_volume	111240 Å³
envelope_diameter	270.5 Å
shell_rg	61.23 Å
envelope_rg	72.82 Å
shape_rg	73.69 Å
total_rg	73.66 Å
total_atoms	67703
n_residues	4242
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

▼

3. P(r) Analysis (GNOM)

dmax	235.2 Å
rg_real	72.53 Å
rg_real_error	1.75 Å
i0_real	3.1500e+09
i0_real_error	6.3730e+07
rg_reciprocal	70.26 Å
i0_reciprocal	3148000000.0000
total_estimate	0.6497
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	67.2 Å
skewness	0.640
kurtosis	-0.048
angular_range	— – 0.1050 Å⁻¹
current_alpha	0.0707
highest_alpha	100500000.0000
n_real_points	22
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 0.996; Sysdev: 0.020; Positv: 1.000; Valcen: 0.991; Smooth: 0.837

▶

4. Crystallography & Experiment

▶

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	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	69507

GMLSLQYPDVYRDETAVQDYHGHKICDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNSYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESSGIAGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRQSPNYRVINIDFRDPEESKWKVLVPEHEKDVLEWIACVRSNFLVLCYLHDVKNILQLHDLTTGALLKTFPLDVGSIVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGILAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVAACANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLVKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQSNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNVDWIP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	{(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone
formula_weight	384.5 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	12

Entity 4 non-polymer

description	THIOCYANATE ION
formula_weight	58.1 kDa
src_method	syn
entity_count	7

Entity 5 non-polymer

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

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	1747

▶

6. Citations (1)

▶

length_a	67.187 Å
length_b	105.735 Å
length_c	155.670 Å
angle_alpha	81.78 °
angle_beta	89.79 °
angle_gamma	89.70 °
z_pdb	6

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.810 Å
resolution_low	29.680 Å
r_factor	—
r_work	0.1907
r_free	0.2489

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

Human prolyl endopeptidase (PREP) - complex with S17092

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