SAXSdb — 3itu

▼

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

;cGMP-dependent 3',5'-cyclic phosphodiesterase ;

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 MAGNESIUM ION × 1 3-ISOBUTYL-1-METHYLXANTHINE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 MAGNESIUM ION × 1 3-ISOBUTYL-1-METHYLXANTHINE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1 MAGNESIUM ION × 1 3-ISOBUTYL-1-METHYLXANTHINE × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 1 MAGNESIUM ION × 1 3-ISOBUTYL-1-METHYLXANTHINE × 1 water × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 MAGNESIUM ION × 2 3-ISOBUTYL-1-METHYLXANTHINE × 2 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 MAGNESIUM ION × 2 3-ISOBUTYL-1-METHYLXANTHINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDE2A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–345； UniProt 579–919 Author chain B； PDBConstruct 5–345； UniProt 579–919 Author chain C； PDBConstruct 5–345； UniProt 579–919 Author chain D； PDBConstruct 5–345； UniProt 579–919

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3itu
Deposition date deposition_date	2009-08-28
Structure title title	hPDE2A catalytic domain complexed with IBMX
Keywords keywords	zn-binding, all-alpha-helical, Alternative splicing, cGMP, Hydrolase, Membrane, Polymorphism; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3itu__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3itu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3itu__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.77 Å
Rg (electron density)	20.77 Å
Total Rg	21.59 Å
Atom count	2785
Residues	338
Excluded volume	49590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3itu__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3itu__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3itu__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3itu__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3itu__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3itu__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;cGMP-dependent 3',5'-cyclic phosphodiesterase ;
Molecular weight formula_weight	40225.1 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	12700

GSAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

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 non-polymer

Description description	3-ISOBUTYL-1-METHYLXANTHINE
Molecular weight formula_weight	222.2 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	1777

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3itua_
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.211.1.0 — automated matches

Domain ID domain_id	d3itub_
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.211.1.0 — automated matches

Domain ID domain_id	d3ituc_
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.211.1.0 — automated matches

Domain ID domain_id	d3itud_
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.211.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3ituA00
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	3ituB00
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	3ituC01
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	3ituD01
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

▶

Unit-cell length a length_a	55.815 Å
Unit-cell length b length_b	73.287 Å
Unit-cell length c length_c	91.532 Å
Unit-cell angle α angle_alpha	109.30 °
Unit-cell angle β angle_beta	88.80 °
Unit-cell angle γ angle_gamma	89.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.580 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1770
R_work r_work	0.1740
R_free r_free	0.2330

hPDE2A catalytic domain complexed with IBMX

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

;cGMP-dependent 3',5'-cyclic phosphodiesterase ;

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3itu__assembly_1__model_1

3itu__assembly_1__model_1 | I(q)

3itu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

hPDE2A catalytic domain complexed with IBMX

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

;cGMP-dependent 3',5'-cyclic phosphodiesterase ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3itu__assembly_1__model_1

3itu__assembly_1__model_1 | I(q)

3itu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)