1Y8P

Crystal structure of the PDK3-L2 complex

Structural Biology Knowledgebase: 1Y8P SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.204

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Y8P

Classification: TRANSFERASE

Total Structure Weight: 63301.72

Macromolecule Entities
Molecule Chains Length Organism Details
[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3 A 419 Homo sapiens EC#: 2.7.11.2 IUBMB
Gene Name(s): PDK3 Gene View PDHK3
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex B 128 Homo sapiens EC#: 2.3.1.12 IUBMB
Gene Name(s): DLAT Gene View DLTA

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

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RED
Query on RED

B DIHYDROLIPOIC ACID
C8 H16 O2 S2
IZFHEQBZOYJLPK-SSDOTTSWSA-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 %)
ATP N/A in BindingDB
N/A in BindingMoad
Kd: 840 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.204
  • Space Group: P 65 2 2

Unit Cell:

Length (Å) Angle (°)
a = 120.90 α = 90.00
b = 120.90 β = 90.00
c = 240.09 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-13
  • Released Date: 2005-05-24
  • Deposition author(s): Kato, M., Chuang, J.L., Wynn, R.M., Chuang, D.T.

Revision History

  • 2011-10-05
    Type: Non-polymer description | Details: --
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4