3TZ4

Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/S-alpha-chloroisocaproate complex with ADP

Structural Biology Knowledgebase: 3TZ4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.202

Literature

Macromolecules
Sequence Display for 3TZ4

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 48016.01

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
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
03H
Query on 03H

A (2S)-2-chloro-4-methylpentanoic acid
(S)-alpha-chloroisocaproate (Synonym)
C6 H11 Cl O2
CBQBIPRPIHIKPW-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
03H N/A in BindingDB
N/A in BindingMoad
Kd: 3200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.202
  • Space Group: P 42 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 127.95 α = 90.00
b = 127.95 β = 90.00
c = 73.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-27
  • Released Date: 2012-10-03
  • 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: --