SAXSdb — 1so2

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

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

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 654–1073 Chain B； UniProt 654–1073	Fragment：catalytic domain, residues 654-1073	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 654–1073 Chain D； UniProt 654–1073	Fragment：catalytic domain, residues 654-1073	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

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 1SO2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SOJ CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH IBMX Deposited 2004-03-15	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 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 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 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 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 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 construct 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
9YUD Re-Refined Human Phosphodiesterase 3B complexed with GSK4394835A Deposited 2025-10-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 654–1074（421 aa） Chain B 654–1074（421 aa）	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

3 other PDB entries and 8 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 1–420； UniProt 654–1073 Author chain B； PDBConstruct 1–420； UniProt 654–1073 Author chain C； PDBConstruct 1–420； UniProt 654–1073 Author chain D； PDBConstruct 1–420； UniProt 654–1073

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	1so2
Deposition date deposition_date	2004-03-12
Structure title title	CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B In COMPLEX WITH A DIHYDROPYRIDAZINE INHIBITOR
Keywords keywords	PDE3B PHOSPHODIESTERASE, HYDROLASE; 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	39.94 Å
Radius of gyration Rg (electron density) rg_electron	39.23 Å
Forward intensity I(0) i0	423743000.00
Molecular weight molecular_weight	169360.0 kDa
Excluded volume excluded_volume	211880 Å³
Envelope volume envelope_volume	278280 Å³
Hydration-shell volume shell_volume	58385 Å³
Envelope diameter envelope_diameter	137.3 Å
Shell Rg shell_rg	45.52 Å
Envelope Rg envelope_rg	38.96 Å
Shape Rg shape_rg	39.23 Å
Total Rg total_rg	39.60 Å
Total atoms total_atoms	11930
Residues n_residues	1463
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	129.4 Å
Rg (real space) rg_real	39.83 Å
Rg uncertainty (real space) rg_real_error	1.03 Å
I(0) (real space) i0_real	4.2370e+08
I(0) uncertainty (real space) i0_real_error	7.3930e+06
Rg (reciprocal space) rg_reciprocal	39.91 Å
I(0) (reciprocal space) i0_reciprocal	423800000.0000
Solution quality estimate total_estimate	0.8963
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	51.8 Å
Skewness Skewness skewness	0.216
Kurtosis Kurtosis kurtosis	-0.507
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	138000000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.892

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;cGMP-inhibited 3',5'-cyclic phosphodiesterase B ;
Molecular weight formula_weight	48158.8 kDa
EC 编号 ec_number	3.1.4.17
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12292

EQEVSLDLILVEEYDSLIEKMSNWNFPIFELVEKMGEKSGRILSQVMYTLFQDTGLLEIFKIPTQQFMNYFRALENGYRDIPYHNRIHATDVLHAVWYLTTRPVPGLQQIHNGCGTGNETDSDGRINHGRIAYISSKSCSNPDESYGCLSSNIPALELMALYVAAAMHDYDHPGRTNAFLVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLHLDHVEFKRFRFLVIEAILATDLKKHFDFLAEFNAKANDVNSNGIEWSNENDRLLVCQVCIKLADINGPAKVRDLHLKWTEGIVNEFYEQGDEEANLGLPISPFMDRSSPQLAKLQESFITHIVGPLCNSYDAAGLLPGQWLEAEEDNDTESGDDEDGEELDTEDEEMENNLNPKPPRRKSRRRIFCQLMHHLTENHKIWK

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	1-DEOXY-1-[(2-HYDROXYETHYL)(NONANOYL)AMINO]HEXITOL
Molecular weight formula_weight	365.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLOHEX-1-EN-1-YL]AMINO}PHENYL)-5-METHYL-4,5-DIHYDROPYRIDAZIN-3(2H)-ONE
Molecular weight formula_weight	513.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	362

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1so2a_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.2 — PDEase

Domain ID domain_id	d1so2b_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.2 — PDEase

Domain ID domain_id	d1so2c_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.2 — PDEase

Domain ID domain_id	d1so2d_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.2 — PDEase

CATH v4.4 (4 domains)

Domain ID domain_id	1so2A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1300 — Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
Homologous superfamily homologous superfamily	10 — 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Domain ID domain_id	1so2B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1300 — Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
Homologous superfamily homologous superfamily	10 — 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Domain ID domain_id	1so2C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1300 — Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
Homologous superfamily homologous superfamily	10 — 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Domain ID domain_id	1so2D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1300 — Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
Homologous superfamily homologous superfamily	10 — 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

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8. Citations (1)

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Unit-cell length a length_a	147.482 Å
Unit-cell length b length_b	121.772 Å
Unit-cell length c length_c	126.671 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.74 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2390
R_work r_work	0.2320
R_free r_free	0.2770

fit	/app/data/saxs_computation/so/1so2/1so2.fit
pddf	/app/data/pr_computation/so/1so2/1so2.pr.out
profile	/app/data/saxs_computation/so/1so2/1so2.dat

CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B In COMPLEX WITH A DIHYDROPYRIDAZINE INHIBITOR

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

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

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