1X7W

Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase

Structural Biology Knowledgebase: 1X7W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.147

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1X7W

Classification: OXIDOREDUCTASE

Total Structure Weight: 84200.09

Macromolecule Entities
Molecule Chains Length Organism Details
2-oxoisovalerate dehydrogenase alpha subunit A 400 Homo sapiens EC#: 1.2.4.4 IUBMB
Mutation: S292Q
Gene Name(s): BCKDHA Gene View
2-oxoisovalerate dehydrogenase beta subunit B 342 Homo sapiens EC#: 1.2.4.4 IUBMB
Gene Name(s): BCKDHB Gene View

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TDP
Query on TDP

A THIAMIN DIPHOSPHATE
C12 H18 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

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

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TDP N/A in BindingDB
Kd: 60900 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.147
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 145.67 α = 90.00
b = 145.67 β = 90.00
c = 69.24 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-08-16
  • Released Date: 2004-11-23
  • Deposition author(s): Wynn, R.M., Kato, M., Machius, M., Chuang, J.L., Li, J., Tomchick, D.R., Chuang, D.T.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values