9VKN | pdb_00009vkn

Crystal structure of DhdR in complex with inducer L2HG

• PDB DOI: https://doi.org/10.2210/pdb9VKN/pdb

• Classification: TRANSCRIPTION
• Organism(s): Achromobacter denitrificans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-23 Released: 2025-08-06 
• Deposition Author(s): Sun, P., Wang, B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.240 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of DhdR in complex with inducer L2HG

Sun, P., Wang, B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 33.37 kDa 
• Atom Count: 2,206 
• Modeled Residue Count: 290 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate dehydrogenase complex repressor	A, B	150	Achromobacter denitrificans	Mutation(s): 0  Gene Names: FOC81_30220
UniProt
Find proteins for A0A6N0JVZ6 (Achromobacter denitrificans) Explore A0A6N0JVZ6  Go to UniProtKB:  A0A6N0JVZ6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S2G (Subject of Investigation/LOI)	C [auth A], F [auth B]	(2S)-2-HYDROXYPENTANEDIOIC ACID C5 H8 O5 HWXBTNAVRSUOJR-VKHMYHEASA-N
ZN	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.240 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.984	α = 90
b = 126.984	β = 90
c = 39.776	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Sun, P., Wang, B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release