SAXSdb — 8xww

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

;Isoform PDE5A1 of cGMP-specific 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	2-[(3-chlorophenyl)methyl]-4-oxidanylidene-3~{H}-quinazoline-7-carboxylic acid × 1 ZINC ION × 1 MAGNESIUM ION × 1 water × 1	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 1–349； UniProt 527–875

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	8xww
Deposition date deposition_date	2024-01-16
Last revision last_revision	2025-01-22
Structure title title	Crystal structure of the catalytic domain of human PDE5A complexed with 2-(3-chlorobenzyl)-4-oxo-3,4-dihydroquinazoline-7-carboxylic acid
Keywords keywords	Inhibitor, Complex, Hydrolase; 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.

8xww__assembly_1__model_1

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

Download this curve (.dat)

8xww__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8xww__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.77 Å
Rg (electron density)	18.60 Å
Total Rg	19.54 Å
Atom count	2381
Residues	292
Excluded volume	42642 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8xww__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	;Isoform PDE5A1 of cGMP-specific 3',5'-cyclic phosphodiesterase ;
Molecular weight formula_weight	40266.2 kDa
EC 编号 ec_number	3.1.4.35
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2448

SYHASAAEEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQEKMLINGESGQAKRN

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	2-[(3-chlorophenyl)methyl]-4-oxidanylidene-3~{H}-quinazoline-7-carboxylic acid
Molecular weight formula_weight	314.7 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

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	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	67

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Unit-cell length a length_a	74.261 Å
Unit-cell length b length_b	74.261 Å
Unit-cell length c length_c	131.943 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	trigonal

Resolution resolution	2.460 Å
Low-resolution limit resolution_low	23.910 Å
R factor r_factor	—
R_work r_work	0.2351
R_free r_free	0.2672

Crystal structure of the catalytic domain of human PDE5A complexed with 2-(3-chlorobenzyl)-4-oxo-3,4-dihydroquinazoline-7-carboxylic acid

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

;Isoform PDE5A1 of cGMP-specific 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

8xww__assembly_1__model_1

8xww__assembly_1__model_1 | I(q)

8xww__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

7. Citations (1)

Crystal structure of the catalytic domain of human PDE5A complexed with 2-(3-chlorobenzyl)-4-oxo-3,4-dihydroquinazoline-7-carboxylic acid

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

;Isoform PDE5A1 of cGMP-specific 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

8xww__assembly_1__model_1

8xww__assembly_1__model_1 | I(q)

8xww__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

7. Citations (1)