9G86 | pdb_00009g86

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

PDB DOI: https://doi.org/10.2210/pdb9G86/pdb

Classification: SIGNALING PROTEIN
Organism(s): Caulobacter vibrioides
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-23 Released: 2025-08-06
Deposition Author(s): Dugelay, C., Jaboulay, C., Guzzo, M., Terradot, L.
Funding Organization(s): ATIP-Avenir

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.229 (Depositor), 0.232 (DCC)
R-Value Work:
0.190 (Depositor), 0.192 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

Dugelay, C., Jaboulay, C., Guzzo, M., Terradot, L.

To be published.

Macromolecule Content

Total Structure Weight: 206.59 kDa
Atom Count: 14,126
Modeled Residue Count: 1,789
Deposited Residue Count: 1,812
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator PleD	A, B, C, D	453	Caulobacter vibrioides	Mutation(s): 0 Gene Names: pleD, CC_2462 EC: 2.7.7.65
UniProt
Find proteins for Q9A5I5 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore Q9A5I5 Go to UniProtKB: Q9A5I5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9A5I5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2E (Subject of Investigation/LOI) Query on C2E Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A] H [auth B] I [auth B] J [auth B] M [auth C] E [auth A], H [auth B], I [auth B], J [auth B], M [auth C], P [auth D], R [auth D], S [auth D]	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) C₂₀ H₂₄ N₁₀ O₁₄ P₂ PKFDLKSEZWEFGL-MHARETSRSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain R [auth D] Focus chain S [auth D]
0O2 (Subject of Investigation/LOI) Query on 0O2 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	F [auth A], K [auth B], N [auth C], Q [auth D]	guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate) C₁₀ H₁₈ N₅ O₂₀ P₅ KCPMACXZAITQAX-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D]	G [auth A], L [auth B], O [auth C], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain T [auth D]