SAXSdb — 9q5g

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1. Structure Basics

entry_id	9q5g
deposition_date	2025-08-20
title	Human prolyl endopeptidase (PREP) - apo form
keywords	apo form, peptide cleavage, HYDROLASE; HYDROLASE
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	52.68 Å
rg_electron	53.31 Å
i0	841424000.00
molecular_weight	243640.0 kDa
excluded_volume	305540 Å³
envelope_volume	418310 Å³
shell_volume	71710 Å³
envelope_diameter	180.5 Å
shell_rg	49.04 Å
envelope_rg	52.61 Å
shape_rg	53.31 Å
total_rg	53.19 Å
total_atoms	17183
n_residues	2120
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	168.4 Å
rg_real	53.20 Å
rg_real_error	1.94 Å
i0_real	8.4140e+08
i0_real_error	1.7250e+07
rg_reciprocal	52.23 Å
i0_reciprocal	840300000.0000
total_estimate	0.7785
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	44.9 Å
skewness	0.586
kurtosis	-0.443
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	228200000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.889; Smooth: 0.003

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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	19676

GMLSLQYPDVYRDETAVQDYHGHKICDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNSYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESSGIAGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRQSPNYRVINIDFRDPEESKWKVLVPEHEKDVLEWIACVRSNFLVLCYLHDVKNILQLHDLTTGALLKTFPLDVGSIVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGILAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVAACANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLVKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQSNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNVDWIP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	9

Entity 3 non-polymer

description	THIOCYANATE ION
formula_weight	58.1 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	11

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	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2284

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6. Citations (1)

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length_a	106.124 Å
length_b	66.880 Å
length_c	158.024 Å
angle_alpha	90.00 °
angle_beta	100.29 °
angle_gamma	90.00 °
z_pdb	6

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.630 Å
resolution_low	34.500 Å
r_factor	0.1535
r_work	0.1511
r_free	0.1998

fit	/app/data/saxs_computation/q5/9q5g/9q5g.fit
pddf	/app/data/pr_computation/q5/9q5g/9q5g.pr.out
profile	/app/data/saxs_computation/q5/9q5g/9q5g.dat

Human prolyl endopeptidase (PREP) - apo form

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