4E02 | pdb_00004e02

Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/(S)-2-chloro-3-phenylpropanoic acid complex with AMPPNP

• PDB DOI: https://doi.org/10.2210/pdb4E02/pdb

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


• Deposited: 2012-03-02 Released: 2013-03-13 
• 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: 
  0.211 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structures of branched-chain alpha-ketoacid dehydrogenase kinase-inhibitor complexes

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.

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.13 kDa 
• Atom Count: 2,676 
• Modeled Residue Count: 307 
• 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
ANP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
WJ1	D [auth A]	(S)-2-chloro-3-phenylpropanoic acid C9 H9 Cl O2 LIDRHDRWTSPELB-QMMMGPOBSA-N
K	C [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:  0.211 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.462	α = 90
b = 127.462	β = 90
c = 73.499	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: 2013-03-13 
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: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description