9G85 | pdb_00009g85

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

PDB DOI: https://doi.org/10.2210/pdb9G85/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): Jaboulay, C., Dugelay, C., Guzzo, M., Terradot, L.
Funding Organization(s): ATIP-Avenir

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.239 (Depositor), 0.237 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)
R-Value Observed:
0.203 (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 ppGpp

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

To be published.

Macromolecule Content

Total Structure Weight: 206.89 kDa
Atom Count: 14,051
Modeled Residue Count: 1,774
Deposited Residue Count: 1,816
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator PleD	A, B, C, D	454	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D]	E [auth A] I [auth B] J [auth B] L [auth B] P [auth C] E [auth A], I [auth B], J [auth B], L [auth B], P [auth C], Q [auth C], R [auth C], V [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 I [auth B] Focus chain J [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain V [auth D]
G4P (Subject of Investigation/LOI) Query on G4P Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D]	F [auth A], K [auth B], S [auth C], W [auth D]	GUANOSINE-5',3'-TETRAPHOSPHATE C₁₀ H₁₇ N₅ O₁₇ P₄ BUFLLCUFNHESEH-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain S [auth C] Focus chain W [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain X [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth D]	G [auth A] H [auth A] M [auth B] N [auth B] O [auth C] G [auth A], H [auth A], M [auth B], N [auth B], O [auth C], T [auth C], U [auth D], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain X [auth D]