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9g85

Structure of Response regulator PleD in complex with c-diGMP and ppGpp

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

Response regulator PleD

Caulobacter vibrioides

UniProt Q9A5I5

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 ;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ; × 4 GUANOSINE-5',3'-TETRAPHOSPHATE × 2 MAGNESIUM ION × 4 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 ;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ; × 4 GUANOSINE-5',3'-TETRAPHOSPHATE × 2 MAGNESIUM ION × 4 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1w25 2v0n 2wb4 9g85 9g85 9g86 9g86

7 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name PLED_CAUVC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–454； UniProt 1–454 Author chain B； PDBConstruct 1–454； UniProt 1–454 Author chain C； PDBConstruct 1–454； UniProt 1–454 Author chain D； PDBConstruct 1–454； UniProt 1–454

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_id9g85
Deposition date deposition_date2024-07-23
Last revision last_revision2025-08-06
Structure title titleStructure of Response regulator PleD in complex with c-diGMP and ppGpp
Keywords keywordsinhibitor complex, SIGNALING PROTEIN; SIGNALING PROTEIN
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.

9g85__assembly_1__model_1

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

Download this curve (.dat)

9g85__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

9g85__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）31.33 Å
Rg (electron density)30.23 Å
Total Rg31.02 Å
Atom count7003
Residues886
Excluded volume123310 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9g85__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 9g85__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 (5)

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7. Citations (1)