2W93

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Allosteric Activation of Pyruvate Decarboxylases. A Never-Ending Story.

Konig, S.Spinka, M.Kutter, S.

(2014) J.Mol.Catal., B Enzym. 61: 100


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRUVATE DECARBOXYLASE ISOZYME 1
A, B, C, D
563Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: PDC1
EC: 4.1.1.-, 4.1.1.43, 4.1.1.72, 4.1.1.74
Find proteins for P06169 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P06169
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download SDF File 
Download CCD File 
A, B, C, D
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
PY0
Query on PY0

Download SDF File 
Download CCD File 
A, B, C, D
(1S,2S)-1-amino-1,2-dihydroxypropan-1-olate
C3 H8 N O3
ISJWJWXATCJUBY-STHAYSLISA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 73.050α = 89.23
b = 79.220β = 73.32
c = 109.090γ = 62.43
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-03
    Type: Initial release
  • Version 1.1: 2014-07-30
    Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2019-01-30
    Type: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-02-06
    Type: Data collection, Experimental preparation