SAXSdb — 5j48

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

cGMP-dependent protein kinase 1

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	1,2-ETHANEDIOL × 4 ;2-amino-8-[(4-chlorophenyl)sulfanyl]-9-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-3,9-dihydro-6H-purin-6-one ; × 1 SODIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 4 ;2-amino-8-[(4-chlorophenyl)sulfanyl]-9-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-3,9-dihydro-6H-purin-6-one ; × 1 SODIUM ION × 1 CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KGP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–135； UniProt 204–336 Author chain B； PDBConstruct 3–135； UniProt 204–336

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	5j48
Deposition date deposition_date	2016-03-31
Structure title title	PKG I's Carboyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-pCPT-cGMP
Keywords keywords	;Binding Sites, Cyclic AMP, Cyclic GMP, Cyclic GMP-Dependent Protein Kinase Type II, Mutagenesis, Site-Directed, Protein Binding, analogs ;; 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.

5j48__assembly_1__model_1

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

Download this curve (.dat)

5j48__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5j48__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.72 Å
Rg (electron density)	14.45 Å
Total Rg	15.64 Å
Atom count	2043
Residues	131
Excluded volume	18600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5j48__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5j48__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 (6)

Entity 1 Entity 1 polymer

Description description	cGMP-dependent protein kinase 1
Molecular weight formula_weight	14986.7 kDa
EC 编号 ec_number	2.7.11.12
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	4410

GSTGLIKHTEYMEFLKSVPTFQSLPEEILSKLADVLEETHYENGEYIIRQGARGDTFFIISKGTVNVTREDSPSEDPVFLRTLGKGDWFGEKALQGEDVRTANVIAAEAVTCLVIDRDSFKHLIGGLDDVSNKAY

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	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	;2-amino-8-[(4-chlorophenyl)sulfanyl]-9-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-3,9-dihydro-6H-purin-6-one ;
Molecular weight formula_weight	487.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	280

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5j48a1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.3 — cAMP-binding domain-like
Family Family family	b.82.3.0 — automated matches

Domain ID domain_id	d5j48a2
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

Domain ID domain_id	d5j48b1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.3 — cAMP-binding domain-like
Family Family family	b.82.3.0 — automated matches

Domain ID domain_id	d5j48b2
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	5j48A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	5j48B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

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Unit-cell length a length_a	35.510 Å
Unit-cell length b length_b	59.240 Å
Unit-cell length c length_c	67.320 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.17 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.490 Å
Low-resolution limit resolution_low	34.952 Å
R factor r_factor	0.1646
R_work r_work	0.1634
R_free r_free	0.1891

PKG I's Carboyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-pCPT-cGMP

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

cGMP-dependent protein kinase 1

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

5j48__assembly_1__model_1

5j48__assembly_1__model_1 | I(q)

5j48__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

PKG I's Carboyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-pCPT-cGMP

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

cGMP-dependent protein kinase 1

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

5j48__assembly_1__model_1

5j48__assembly_1__model_1 | I(q)

5j48__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)