6EFH

Pyruvate decarboxylase from Kluyveromyces lactis soaked with pyruvamide

• PDB DOI: https://doi.org/10.2210/pdb6EFH/pdb

• Classification: LYASE
• Organism(s): Kluyveromyces lactis NRRL Y-1140
• Mutation(s): No 


• Deposited: 2018-08-16 Released: 2018-08-29 
• Deposition Author(s): Kutter, S., Konig, S.

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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

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 124.78 kDa 
• Atom Count: 8,712 
• Modelled Residue Count: 1,113 
• Deposited Residue Count: 1,126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate decarboxylase	A, B	563	Kluyveromyces lactis NRRL Y-1140	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	D [auth A], H [auth B]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
1PE	F [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PY0	C [auth A], G [auth B]	(1S,2S)-1-amino-1,2-dihydroxypropan-1-olate C3 H8 N O3 ISJWJWXATCJUBY-STHAYSLISA-N
MG	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 = 172.765	α = 90
b = 172.765	β = 90
c = 210.083	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Kutter, S., Konig, S.

Revision History  

• 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