SAXSdb — 5e80

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

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

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	N-(3-chloro-2-methylphenyl)-4-(3,4-dimethyl-7-oxo-2-phenyl-2,7-dihydro-6H-pyrazolo[3,4-d]pyridazin-6-yl)butanamide × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	N-(3-chloro-2-methylphenyl)-4-(3,4-dimethyl-7-oxo-2-phenyl-2,7-dihydro-6H-pyrazolo[3,4-d]pyridazin-6-yl)butanamide × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDE6D_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 2–150 Author chain B； PDBConstruct 1–149； UniProt 2–150

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	5e80
Deposition date deposition_date	2015-10-13
Structure title title	The crystal structure of PDEd in complex with inhibitor-2a
Keywords keywords	Prenyl binding Protein /inhibitor, Immunoglobulin-like beta-sandwich, GDI-like solubilizing factor, lipid binding protein; LIPID BINDING PROTEIN
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.

5e80__assembly_1__model_1

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

Download this curve (.dat)

5e80__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5e80__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.80 Å
Rg (electron density)	15.64 Å
Total Rg	16.90 Å
Atom count	1246
Residues	149
Excluded volume	22303 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5e80__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5e80__assembly_2__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta ;
Molecular weight formula_weight	17251.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	2503

SAKDERAREILRGFKLNWMNLRDAATGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N-(3-chloro-2-methylphenyl)-4-(3,4-dimethyl-7-oxo-2-phenyl-2,7-dihydro-6H-pyrazolo[3,4-d]pyridazin-6-yl)butanamide
Molecular weight formula_weight	449.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	15

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5e80a_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.8 — RhoGDI-like

Domain ID domain_id	d5e80b_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.8 — RhoGDI-like

CATH v4.4 (2 domains)

Domain ID domain_id	5e80A00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	50 — Coagulation Factor XIII; Chain A, domain 1
Homologous superfamily homologous superfamily	40 — GMP phosphodiesterase, delta subunit

Domain ID domain_id	5e80B00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	50 — Coagulation Factor XIII; Chain A, domain 1
Homologous superfamily homologous superfamily	40 — GMP phosphodiesterase, delta subunit

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Unit-cell length a length_a	31.760 Å
Unit-cell length b length_b	40.900 Å
Unit-cell length c length_c	68.800 Å
Unit-cell angle α angle_alpha	97.70 °
Unit-cell angle β angle_beta	102.38 °
Unit-cell angle γ angle_gamma	89.31 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	26.060 Å
R factor r_factor	0.1884
R_work r_work	0.1853
R_free r_free	0.2473

The crystal structure of PDEd in complex with inhibitor-2a

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

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

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

5e80__assembly_1__model_1

5e80__assembly_1__model_1 | I(q)

5e80__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The crystal structure of PDEd in complex with inhibitor-2a

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

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

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

5e80__assembly_1__model_1

5e80__assembly_1__model_1 | I(q)

5e80__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)