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5jd7

PKG I's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with PET-cGMP

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

cGMP-dependent protein kinase 1

Homo sapiens

UniProt Q13976

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 ;3-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-6-phenyl-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one ; × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
4ku7 4ku8 4ku8 4ku8 4qx5 4qxk 4z07 5j48 5j48 5jax 5jd7 5l0n

30 assemblies; showing the first 12

Homodimer
1zxa 4r4l 4r4l 4r4m 4r4m 4z07 7lv3

7 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name KGP1_HUMAN
Isoform Q13976-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–135； UniProt 220–352

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_id5jd7
Deposition date deposition_date2016-04-15
Structure title titlePKG I's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with PET-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 methodX-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.

5jd7__assembly_1__model_1

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

Download this curve (.dat)

5jd7__assembly_1__model_1 | I(q)

10-2 10-1 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5jd7__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）15.38 Å
Rg (electron density)14.03 Å
Total Rg15.43 Å
Atom count1937
Residues126
Excluded volume17839 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5jd7__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 (3)

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5jd7a_
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.3 — cAMP-binding domain-like
Family Family familyb.82.3.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id5jd7A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
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7. Citations (1)