1PYD

CATALYTIC CENTERS IN THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE AT 2.4 ANGSTROMS RESOLUTION

Structural Biology Knowledgebase: 1PYD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Observed: 0.197

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1PYD

Classification: LYASE(CARBON-CARBON)

Total Structure Weight: 122643.25

Macromolecule Entities
Molecule Chains Length Organism Details
PYRUVATE DECARBOXYLASE A, B 556 Saccharomyces cerevisiae EC#: 4.1.1.1 IUBMB
Mutation: R55A, C143A, V206A, A208V, V538I, E551K
Gene Name(s): PDC1 YLR044C L2104
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Observed: 0.197
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 141.95 α = 90.00
b = 74.67 β = 116.39
c = 119.95 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1993-03-23
  • Released Date: 1994-04-30
  • Deposition author(s): Furey, W., Dyda, F.

Revision History

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