4H7Q

Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase in complex with alpha-ketoisocaproic acid and ADP

Structural Biology Knowledgebase: 4H7Q SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.209

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4H7Q

Classification: transferase / transferase inhibitor

Total Structure Weight: 47995.55

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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
COI
Query on COI

A 2-OXO-4-METHYLPENTANOIC ACID
alpha-ketoisocaproic acid (Synonym)
C6 H10 O3
BKAJNAXTPSGJCU-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

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

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
COI N/A in BindingDB
N/A in BindingMoad
Kd: 8800 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.209
  • Space Group: P 42 21 2

Unit Cell:

Length (Å) Angle (°)
a = 128.52 α = 90.00
b = 128.52 β = 90.00
c = 73.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-20
  • Released Date: 2013-06-05
  • Deposition author(s): Tso, S.C., Chuang, J.L., Gui, W.J., Wynn, R.M., Li, J., Chuang, D.T.

Revision History

No revisions since initial release