4E00 | pdb_00004e00

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

• PDB DOI: https://doi.org/10.2210/pdb4E00/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-03-01 Released: 2013-03-27 
• Deposition Author(s): Tso, S.C., Chuang, J.L., Gui, W.J., Wynn, R.M., Li, J., Chuang, D.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.234 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

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

Tso, S.C., Chuang, J.L., Gui, W.J., Wynn, R.M., Li, J., 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: 48.11 kDa 
• Atom Count: 2,607 
• Modeled Residue Count: 308 
• 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): 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 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	C [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	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.234 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.057	α = 90
b = 128.057	β = 90
c = 73.775	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	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: 2013-03-27 
Deposition Author(s): Tso, S.C., Chuang, J.L., Gui, W.J., Wynn, R.M., Li, J., Chuang, D.T.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations