7q9s

Crystal structure of PDE6D KRas peptide complex with Compound-1

Method: X-RAY DIFFRACTION

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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 heterocomplex	Heteromer	Protein 2	KRas × 1 2-methyl-3-(1~{H}-pyrazol-5-yl)imidazo[1,2-a]pyridine × 1 SULFATE ION × 1 1,2-ETHANEDIOL × 4 FARNESYL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	KRas × 1 2-methyl-3-(1~{H}-pyrazol-5-yl)imidazo[1,2-a]pyridine × 1 1,2-ETHANEDIOL × 3 DIMETHYL SULFOXIDE × 1 FARNESYL × 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 AAA； PDBConstruct 1–150； UniProt 1–150 Author chain BBB； PDBConstruct 1–150； UniProt 1–150

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	7q9s
Deposition date deposition_date	2021-11-14
Structure title title	Crystal structure of PDE6D KRas peptide complex with Compound-1
Keywords keywords	Complex, Inhibitor, PROTEIN BINDING; PROTEIN BINDING
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.

7q9s__assembly_1__model_1

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

Download this curve (.dat)

7q9s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7q9s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.04 Å
Rg (electron density)	15.76 Å
Total Rg	16.98 Å
Atom count	1294
Residues	153
Excluded volume	23289 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7q9s__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7q9s__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 (8)

Entity 1 Entity 1 polymer

Description description	;Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta ;
Molecular weight formula_weight	17441.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	BBB,AAA
Atom count atom_count	2967

MSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV

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	KRas
Molecular weight formula_weight	1528.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	CCC,DDD

DGKKKKKKSKTKC

Entity 3 Entity 3 non-polymer

Description description	2-methyl-3-(1~{H}-pyrazol-5-yl)imidazo[1,2-a]pyridine
Molecular weight formula_weight	198.2 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	nat
Copy count entity_count	7

Entity 6 Entity 6 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	FARNESYL
Molecular weight formula_weight	206.4 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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Unit-cell length a length_a	77.104 Å
Unit-cell length b length_b	81.123 Å
Unit-cell length c length_c	118.514 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	1.850 Å
Low-resolution limit resolution_low	40.657 Å
R factor r_factor	—
R_work r_work	0.1993
R_free r_free	0.2273

Crystal structure of PDE6D KRas peptide complex with Compound-1

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

7q9s__assembly_1__model_1

7q9s__assembly_1__model_1 | I(q)

7q9s__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal structure of PDE6D KRas peptide complex with Compound-1

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

7q9s__assembly_1__model_1

7q9s__assembly_1__model_1 | I(q)

7q9s__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)