SAXSdb — 9yud

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1. Protein Identity and Related Structures Protein Identity & Related Structures

;cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B ;

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 654–1074 Chain B； UniProt 654–1074	Not recorded	X5W [3-[(4,7-dimethoxyquinolin-2-yl)carbonylamino]-5-[methyl-(phenylmethyl)carbamoyl]phenyl]-oxidanyl-oxidanylidene-boron × 1 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M NaCl, 25%PEG3350,0.1 M bis-Tris pH 6.5, cryo: 25% ethylene glycol	Resolution 2.70 Å R-free 0.238

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9YUD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SO2 CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B In COMPLEX WITH A DIHYDROPYRIDAZINE INHIBITOR Deposited 2004-03-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073 Chain B 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073	Not recorded	MG MAGNESIUM ION × 5 HG9 1-DEOXY-1-[(2-HYDROXYETHYL)(NONANOYL)AMINO]HEXITOL × 4 666 6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLOHEX-1-EN-1-YL]AMINO}PHENYL)-5-METHYL-4,5-DIHYDROPYRIDAZIN-3(2H)-ONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Peg MMe, MES, MAgnesium Sulfate, HEGA-9, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.277
1SO2 CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B In COMPLEX WITH A DIHYDROPYRIDAZINE INHIBITOR Deposited 2004-03-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073 Chain D 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073	Not recorded	MG MAGNESIUM ION × 4 666 6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLOHEX-1-EN-1-YL]AMINO}PHENYL)-5-METHYL-4,5-DIHYDROPYRIDAZIN-3(2H)-ONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Peg MMe, MES, MAgnesium Sulfate, HEGA-9, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.277
1SOJ CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH IBMX Deposited 2004-03-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073 Chain B 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073	Not recorded	MG MAGNESIUM ION × 4 IBM 3-ISOBUTYL-1-METHYLXANTHINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Peg MME, MES, MAgnesium Sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.90 Å R-free 0.249
1SOJ CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH IBMX Deposited 2004-03-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073 Chain D 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073	Not recorded	MG MAGNESIUM ION × 4 IBM 3-ISOBUTYL-1-METHYLXANTHINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Peg MME, MES, MAgnesium Sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.90 Å R-free 0.249
1SOJ CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH IBMX Deposited 2004-03-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073 Chain F 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073	Not recorded	MG MAGNESIUM ION × 4 IBM 3-ISOBUTYL-1-METHYLXANTHINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Peg MME, MES, MAgnesium Sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.90 Å R-free 0.249
1SOJ CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH IBMX Deposited 2004-03-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073 Chain H 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073	Not recorded	MG MAGNESIUM ION × 4 IBM 3-ISOBUTYL-1-METHYLXANTHINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Peg MME, MES, MAgnesium Sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.90 Å R-free 0.249
1SOJ CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH IBMX Deposited 2004-03-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073 Chain J 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073	Not recorded	MG MAGNESIUM ION × 4 IBM 3-ISOBUTYL-1-METHYLXANTHINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Peg MME, MES, MAgnesium Sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.90 Å R-free 0.249
1SOJ CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH IBMX Deposited 2004-03-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain K 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073 Chain L 654–1073（420 aa） Fragment：catalytic domain, residues 654-1073	Not recorded	MG MAGNESIUM ION × 4 IBM 3-ISOBUTYL-1-METHYLXANTHINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Peg MME, MES, MAgnesium Sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.90 Å R-free 0.249
8SYC Crystal structure of PDE3B in complex with GSK4394835A Deposited 2023-05-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 654–1074（421 aa） Chain D 654–1074（421 aa）	Mutation：K691D, R783D, A831E, K880E, S981D Mutation：K691D, R783D, A831E, K880E, S981D	MG MAGNESIUM ION × 4 X5W [3-[(4,7-dimethoxyquinolin-2-yl)carbonylamino]-5-[methyl-(phenylmethyl)carbamoyl]phenyl]-oxidanyl-oxidanylidene-boron × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M NaCl, 25%PEG3350,0.1 M bis-Tris pH6.5, cryo: 25% ethylene glycol	Resolution 2.70 Å R-free 0.224

3 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PDE3B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–422； UniProt 654–1074 Author chain B； PDBConstruct 2–422； UniProt 654–1074

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yud
Deposition date deposition_date	2025-10-22
Structure title title	Re-Refined Human Phosphodiesterase 3B complexed with GSK4394835A
Keywords keywords	hydrolase, phosphodiesterase, inhibitor, covalent, boronate; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	29.12 Å
Radius of gyration Rg (electron density) rg_electron	28.17 Å
Forward intensity I(0) i0	94034000.00
Molecular weight molecular_weight	77425.0 kDa
Excluded volume excluded_volume	96952 Å³
Envelope volume envelope_volume	117610 Å³
Hydration-shell volume shell_volume	34186 Å³
Envelope diameter envelope_diameter	93.3 Å
Shell Rg shell_rg	36.01 Å
Envelope Rg envelope_rg	28.04 Å
Shape Rg shape_rg	28.18 Å
Total Rg total_rg	28.90 Å
Total atoms total_atoms	5482
Residues n_residues	709
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	89.5 Å
Rg (real space) rg_real	29.06 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	9.4030e+07
I(0) uncertainty (real space) i0_real_error	1.3760e+06
Rg (reciprocal space) rg_reciprocal	29.09 Å
I(0) (reciprocal space) i0_reciprocal	94040000.0000
Solution quality estimate total_estimate	0.9099
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	31.5 Å
Skewness Skewness skewness	0.228
Kurtosis Kurtosis kurtosis	-0.610
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20580000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B ;
Molecular weight formula_weight	51054.5 kDa
EC 编号 ec_number	3.1.4.17
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5527

MEQEVSLDLILVEEYDSLIEKMSNWNFPIFELVEKMGEDSGRILSQVMYTLFQDTGLLEIFKIPTQQFMNYFRALENGYRDIPYHNRIHATDVLHAVWYLTTRPVPGLQQIHNGCGTGNETDSDGRINHGDIAYISSKSCSNPDESYGCLSSNIPALELMALYVAAAMHDYDHPGRTNEFLVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLHLDHVEFERFRFLVIEAILATDLKKHFDFLAEFNAKANDVNSNGIEWSNENDRLLVCQVCIKLADINGPAKVRDLHLKWTEGIVNEFYEQGDEEANLGLPISPFMDRSDPQLAKLQESFITHIVGPLCNSYDAAGLLPGQWLEAEEDNDTESGDDEDGEELDTEDEEMENNLNPKPPRRKSRRRIFCQLMHHLTENHKIWKENLYFQGDYKDDDDKGHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	45

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8. Citations (2)

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Unit-cell length a length_a	78.586 Å
Unit-cell length b length_b	78.586 Å
Unit-cell length c length_c	166.339 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	71.060 Å
R factor r_factor	0.1892
R_work r_work	0.1868
R_free 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

;cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B ;

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)