3DVA

Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex

Structural Biology Knowledgebase: 3DVA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3DVA

Classification: OXIDOREDUCTASE / TRANSFERASE

Total Structure Weight: 402592.41

Macromolecule Entities
Molecule Chains Length Organism Details
Pyruvate dehydrogenase E1 component subunit alpha A, C, E, G 369 Geobacillus stearothermophilus EC#: 1.2.4.1 IUBMB
Mutation: I206A
Gene Name(s): pdhA
Pyruvate dehydrogenase E1 component subunit beta B, D, F, H 325 Geobacillus stearothermophilus EC#: 1.2.4.1 IUBMB
Gene Name(s): pdhB
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex I, J 428 Geobacillus stearothermophilus EC#: 2.3.1.12 IUBMB
Gene Name(s): pdhC

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

A, C, E, G 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]- 3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE
3-DEAZA-THDP (Synonym)
C13 H19 N3 O7 P2 S
IOGGWTLVIZLGGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

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

A, C, E, G MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.190
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.67 α = 90.00
b = 232.29 β = 91.20
c = 91.94 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-07-18
  • Released Date: 2009-01-13
  • Deposition author(s): Pei, X.Y., Titman, C.M., Frank, R.A.W., Leeper, F.J., Luisi, B.F.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4