4DZY

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

Structural Biology Knowledgebase: 4DZY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DZY

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 48050.03

Macromolecule Entities
Molecule Chains Length Organism Details
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial A 418 Rattus norvegicus EC#: 2.7.11.4 IUBMB
Gene Name(s): Bckdk

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
JSmol
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
WJ1
Query on WJ1

A (S)-2-chloro-3-phenylpropanoic acid
C9 H9 Cl O2
LIDRHDRWTSPELB-QMMMGPOBSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
WJ1 N/A in BindingDB
N/A in BindingMoad
Kd: 2400 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.205
  • Space Group: P 42 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 127.33 α = 90.00
b = 127.33 β = 90.00
c = 73.25 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-01
  • 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

  • 2013-05-29
    Type: Citation | Details: --