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9yud

Re-Refined Human Phosphodiesterase 3B complexed with GSK4394835A

Method: X-RAY DIFFRACTION D_max: 89.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yud
deposition_date	2025-10-22
title	Re-Refined Human Phosphodiesterase 3B complexed with GSK4394835A
keywords	hydrolase, phosphodiesterase, inhibitor, covalent, boronate; 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	29.12 Å
rg_electron	28.17 Å
i0	94034000.00
molecular_weight	77425.0 kDa
excluded_volume	96952 Å³
envelope_volume	117610 Å³
shell_volume	34186 Å³
envelope_diameter	93.3 Å
shell_rg	36.01 Å
envelope_rg	28.04 Å
shape_rg	28.18 Å
total_rg	28.90 Å
total_atoms	5482
n_residues	709
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	89.5 Å
rg_real	29.06 Å
rg_real_error	0.66 Å
i0_real	9.4030e+07
i0_real_error	1.3760e+06
rg_reciprocal	29.09 Å
i0_reciprocal	94040000.0000
total_estimate	0.9099
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	31.5 Å
skewness	0.228
kurtosis	-0.610
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	20580000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.938

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	;cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B ;
formula_weight	51054.5 kDa
ec_number	3.1.4.17
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5527

MEQEVSLDLILVEEYDSLIEKMSNWNFPIFELVEKMGEDSGRILSQVMYTLFQDTGLLEIFKIPTQQFMNYFRALENGYRDIPYHNRIHATDVLHAVWYLTTRPVPGLQQIHNGCGTGNETDSDGRINHGDIAYISSKSCSNPDESYGCLSSNIPALELMALYVAAAMHDYDHPGRTNEFLVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLHLDHVEFERFRFLVIEAILATDLKKHFDFLAEFNAKANDVNSNGIEWSNENDRLLVCQVCIKLADINGPAKVRDLHLKWTEGIVNEFYEQGDEEANLGLPISPFMDRSDPQLAKLQESFITHIVGPLCNSYDAAGLLPGQWLEAEEDNDTESGDDEDGEELDTEDEEMENNLNPKPPRRKSRRRIFCQLMHHLTENHKIWKENLYFQGDYKDDDDKGHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	[3-[(4,7-dimethoxyquinolin-2-yl)carbonylamino]-5-[methyl-(phenylmethyl)carbamoyl]phenyl]-oxidanyl-oxidanylidene-boron
formula_weight	498.3 kDa
src_method	man
entity_count	1

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	45

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6. Citations (2)

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length_a	78.586 Å
length_b	78.586 Å
length_c	166.339 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 41
int_tables_number	76
crystal_system	—

resolution	2.700 Å
resolution_low	71.060 Å
r_factor	0.1892
r_work	0.1868
r_free	0.2384

fit	/app/data/saxs_computation/yu/9yud/9yud.fit
pddf	/app/data/pr_computation/yu/9yud/9yud.pr.out
profile	/app/data/saxs_computation/yu/9yud/9yud.dat

Re-Refined Human Phosphodiesterase 3B complexed with GSK4394835A

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

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)