6EFH

Pyruvate decarboxylase from Kluyveromyces lactis soaked with pyruvamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The crystal structures of pyruvate decarboxylase from Kluyveromyces lactis in the absence of ligands and in the presence of the substrate surrogate pyruvamide

Kutter, S.Konig, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate decarboxylase
A, B
563Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
EC: 4.1.1.1
UniProt
Find proteins for Q12629 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q12629 
Go to UniProtKB:  Q12629
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12629
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
F [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PY0
Query on PY0

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
(1S,2S)-1-amino-1,2-dihydroxypropan-1-olate
C3 H8 N O3
ISJWJWXATCJUBY-STHAYSLISA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.765α = 90
b = 172.765β = 90
c = 210.083γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary