SAXSdb — 5e8f

▼

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 heterocomplex	Heteromer	Protein 2	;Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' ; × 1 （P51160） GERAN-8-YL GERAN × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	;Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' ; × 1 （P51160） GERAN-8-YL GERAN × 1 water × 2	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 C； PDBConstruct 1–149； UniProt 2–150

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

Homo sapiens

UniProt P51160

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta ; × 1 （O43924） GERAN-8-YL GERAN × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta ; × 1 （O43924） GERAN-8-YL GERAN × 1 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	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–5； UniProt 851–855 Author chain E； PDBConstruct 1–5； UniProt 851–855

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	5e8f
Deposition date deposition_date	2015-10-14
Structure title title	Structure of Fully modified geranylgeranylated PDE6C Peptide in complex with PDE6D
Keywords keywords	Prenyl binding protein, Immunoglobulin-like beta sandwitch fold, geranylgeranyl, hydrolase; 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.

5e8f__assembly_2__model_1

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

Download this curve (.dat)

5e8f__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5e8f__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.03 Å
Rg (electron density)	15.79 Å
Total Rg	16.95 Å
Atom count	1277
Residues	153
Excluded volume	23025 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5e8f__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5e8f__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta ;
Molecular weight formula_weight	17309.8 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,C
Atom count atom_count	2651

SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV

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 polymer

Description description	;Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' ;
Molecular weight formula_weight	581.7 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	D,E

KSKTC

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 3 Entity 3 non-polymer

Description description	GERAN-8-YL GERAN
Molecular weight formula_weight	274.5 kDa
Source method src_method	man
Copy count entity_count	2

Source Source

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	108

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5e8fa_
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	d5e8fc_
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	5e8fA00
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	5e8fC00
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

▶

Unit-cell length a length_a	77.710 Å
Unit-cell length b length_b	81.430 Å
Unit-cell length c length_c	118.530 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	29.630 Å
R factor r_factor	0.2012
R_work r_work	0.1983
R_free r_free	0.2561

Structure of Fully modified geranylgeranylated PDE6C Peptide in complex with PDE6D

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

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

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

5e8f__assembly_2__model_1

5e8f__assembly_2__model_1 | I(q)

5e8f__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of Fully modified geranylgeranylated PDE6C Peptide in complex with PDE6D

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

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

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

5e8f__assembly_2__model_1

5e8f__assembly_2__model_1 | I(q)

5e8f__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)