SAXSdb — 3jwr

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

;cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera ;

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma ; × 1 （P18545） ZINC ION × 1 MAGNESIUM ION × 1 3-ISOBUTYL-1-METHYLXANTHINE × 3 water × 1	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma ; × 1 （P18545） ZINC ION × 1 MAGNESIUM ION × 1 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	PDE5A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–256； UniProt 535–786 Author chain A； PDBConstruct 297–330； UniProt 827–860 Author chain B； PDBConstruct 5–256； UniProt 535–786 Author chain B； PDBConstruct 297–330； UniProt 827–860

;cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera ;

Homo sapiens

UniProt P51160

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma ; × 1 （P18545） ZINC ION × 1 MAGNESIUM ION × 1 3-ISOBUTYL-1-METHYLXANTHINE × 3 water × 1	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma ; × 1 （P18545） ZINC ION × 1 MAGNESIUM ION × 1 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	PDE6C_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 257–296； UniProt 746–785 Author chain B； PDBConstruct 257–296； UniProt 746–785

;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma ;

OrganismNot specified

UniProt P18545

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	;cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera ; × 1 （O76074,P51160） ZINC ION × 1 MAGNESIUM ION × 1 3-ISOBUTYL-1-METHYLXANTHINE × 3 water × 1	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	;cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera ; × 1 （O76074,P51160） ZINC ION × 1 MAGNESIUM ION × 1 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	CNRG_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–18； UniProt 70–87 Author chain D； PDBConstruct 1–18； UniProt 70–87

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	3jwr
Deposition date deposition_date	2009-09-18
Structure title title	Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with 3-isobutyl-1-methylxanthine (IBMX) and PDE6 gamma-subunit inhibitory peptide 70-87.
Keywords keywords	mostly alpha, cGMP, Hydrolase, Polymorphism, Sensory transduction, Vision; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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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.

3jwr__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3jwr__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3jwr__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.09 Å
Rg (electron density)	19.95 Å
Total Rg	20.82 Å
Atom count	2846
Residues	345
Excluded volume	50816 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3jwr__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3jwr__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	;cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera ;
Molecular weight formula_weight	38282.1 kDa
EC 编号 ec_number	3.1.4.35
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	5683

GSHMEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFWEQGDLERTVLQQQPIPMMDRNKRDELPKLQVGFIDFVCTQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma ;
Molecular weight formula_weight	2185.4 kDa
EC 编号 ec_number	3.1.4.17
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

WEAFNHLELHELAQYGII

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	3-ISOBUTYL-1-METHYLXANTHINE
Molecular weight formula_weight	222.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3jwrb1
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	d3jwrb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	3jwrA00
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	3jwrB00
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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Unit-cell length a length_a	47.257 Å
Unit-cell length b length_b	125.651 Å
Unit-cell length c length_c	153.854 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.994 Å
Low-resolution limit resolution_low	40.413 Å
R factor r_factor	0.2155
R_work r_work	0.2120
R_free r_free	0.2797

Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with 3-isobutyl-1-methylxanthine (IBMX) and PDE6 gamma-subunit inhibitory peptide 70-87.

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

;cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera ;

State in the Current Structure

Other States of the Same Protein in the Database

;cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera ;

State in the Current Structure

Other States of the Same Protein in the Database

;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma ;

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

3jwr__assembly_2__model_1

3jwr__assembly_2__model_1 | I(q)

3jwr__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with 3-isobutyl-1-methylxanthine (IBMX) and PDE6 gamma-subunit inhibitory peptide 70-87.

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

;cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma ;

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

3jwr__assembly_2__model_1

3jwr__assembly_2__model_1 | I(q)

3jwr__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)