SAXSdb — 10oz

▼

1. Structure Basics

entry_id	10oz
deposition_date	2026-01-30
title	Structure of PDE5 PDE6 chimera
keywords	Phosphodiesterase, HYDROLASE; HYDROLASE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	44.74 Å
rg_electron	44.58 Å
i0	425891000.00
molecular_weight	172830.0 kDa
excluded_volume	217500 Å³
envelope_volume	296220 Å³
shell_volume	57058 Å³
envelope_diameter	142.4 Å
shell_rg	47.40 Å
envelope_rg	43.70 Å
shape_rg	44.59 Å
total_rg	44.70 Å
total_atoms	12147
n_residues	1493
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	142.6 Å
rg_real	46.25 Å
rg_real_error	0.51 Å
i0_real	4.2260e+08
i0_real_error	5.9320e+06
rg_reciprocal	44.74 Å
i0_reciprocal	425800000.0000
total_estimate	0.6686
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	53.0 Å
skewness	0.370
kurtosis	-0.558
angular_range	— – 0.1750 Å⁻¹
current_alpha	2.2120
highest_alpha	35400000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 0.905; Sysdev: 0.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.206

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	;cGMP-specific 3',5'-cyclic phosphodiesterase PDE5-PDE6 chimera ;
formula_weight	91715.9 kDa
ec_number	3.1.4.35
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	12147

MGEISQETVEKYLEANPQFAKEYFNRKLQVEVPSGGAQAPASASFPGRTLAEEAALYLELLEVLLEEAGSVELAAHRALQRLAQLLQADRCSMFLCRARNGTPEVASKLLDVTPTSKFEDNLVVPDREAVFPLDVGIVGWVAHTKKTFNVPDVKKNSHFSDFMDKQTGYVTRNLLATPIVMGKEVLAVFMAVNKVDASEFSKQDEEVFSKYLSFVSIILKLHHTNYLYNIESRRSQILMWSANKVFEELTDVERQFHKALYTVRTYLNCERYSIGLLDMTKEKEFYDEWPVKLGEVEPYKGPKTPDGREVIFYKIIDYILHGKEEIKVIPTPPMDHWTLISGLPTYVAENGFICNMLNAPADEYFTFQKGPVDETGWVIKNVLSLPIVNKKEDIVGVATFYNRKDGKPFDEYDEHIAETLTQFLGWSLLNTDTYEKMNKLMAKQMVTLEVLSYHASAAEEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCKWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQKRLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIMKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPADLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQEKTLINGESSQTKRN

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Spodoptera aff. frugiperda 1 BOLD-2017

Entity 2 polymer

description	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma ;
formula_weight	11855.6 kDa
ec_number	3.1.4.35
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

MGSSHHHHHHSSGLVPRGSHMNLEPPKAEIRSATRVMGGPVTPRKGPPKFKQRQTRQFKSKPPKKGVQGFGDDIPGMEGLGTDITVICPWEAFNHLELHELAQYGII

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Escherichia coli

Entity 3 non-polymer

description	5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE
formula_weight	474.6 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	CYCLIC GUANOSINE MONOPHOSPHATE
formula_weight	345.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

▶

6. Citations (2)

▶

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	3.060 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.06 Å
resolution_method	—
num_particles	158600

fit	/app/data/saxs_computation/0o/10oz/10oz.fit
pddf	/app/data/pr_computation/0o/10oz/10oz.pr.out
profile	/app/data/saxs_computation/0o/10oz/10oz.dat

Structure of PDE5 PDE6 chimera

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

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)