8F4Q | pdb_00008f4q

rat branched chain ketoacid dehydrogenase kinase in complex with inhibtors

• PDB DOI: https://doi.org/10.2210/pdb8F4Q/pdb

• Classification: SIGNALING PROTEIN,TRANSFERASE/INHIBITOR
• Organism(s): Rattus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-11-11 Released: 2023-12-13 
• Deposition Author(s): Liu, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.234 (Depositor) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Discovery of branched-chain ketoacid dehydrogenase kinase (BDK) inhibitors acting as stabilizers or destabilizers

Roth Flach, R., Filipski, K., Bollinger, E.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.59 kDa 
• Atom Count: 2,700 
• Modeled Residue Count: 319 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial	A	388	Rattus	Mutation(s): 0  Gene Names: Bckdk EC: 2.7.11.4 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt
Find proteins for Q00972 (Rattus norvegicus) Explore Q00972  Go to UniProtKB:  Q00972

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
XER (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A]	3-chloro-5-fluorothieno[3,2-b]thiophene-2-carboxylic acid C7 H2 Cl F O2 S2 UXMBSHHPPVOPJU-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.234 (Depositor) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.67	α = 90
b = 111.67	β = 90
c = 139.34	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Liu, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary