3VAD

Crystal structure of I170F mutant branched-chain alpha-ketoacid dehydrogenase kinase in complex with 3,6-dichlorobenzo[b]thiophene-2-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb3VAD/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-12-29 Released: 2013-01-16 
• Deposition Author(s): Ahmed, K., Gui, W.J., Tso, S.C., Chuang, J.L., Wynn, R.M., Chuang, D.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.276 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

Literature

Crystal structure of I170F mutant branched-chain alpha-ketoacid dehydrogenase kinase in complex with 3,6-dichlorobenzo[b]thiophene-2-carboxylic acid

Ahmed, K., Gui, W.J., Tso, S.C., Chuang, J.L., M Wynn, R., Chuang, D.T.

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.

Macromolecule Content

• Total Structure Weight: 48.39 kDa 
• Atom Count: 2,609 
• Modelled Residue Count: 310 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial	A	418	Rattus norvegicus	Mutation(s): 1  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
0F1	E [auth A], F [auth A]	3,6-dichloro-1-benzothiophene-2-carboxylic acid C9 H4 Cl2 O2 S AAHPIJMQJAZYTM-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.276 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.079	α = 90
b = 128.079	β = 90
c = 74.035	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Ahmed, K., Gui, W.J., Tso, S.C., Chuang, J.L., Wynn, R.M., Chuang, D.T.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2014-10-08
  Changes: Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations