2VK4 | pdb_00002vk4

Crystal structure of pyruvate decarboxylase from Kluyveromyces lactis

PDB DOI: https://doi.org/10.2210/pdb2VK4/pdb
Entry: 2VK4 supersedes: 2G1I

Classification: LYASE
Organism(s): Kluyveromyces lactis
Mutation(s): No

Deposited: 2007-12-17 Released: 2009-01-27
Deposition Author(s): Kutter, S., Relle, S., Wille, G., Weiss, M.S., Konig, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.230 (Depositor), 0.229 (DCC)
R-Value Work:
0.178 (Depositor), 0.177 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 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

DOI: https://doi.org/10.1016/J.MOLCATB.2009.02.010

Macromolecule Content

Total Structure Weight: 248.67 kDa
Atom Count: 18,654
Modeled Residue Count: 2,232
Deposited Residue Count: 2,252
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRUVATE DECARBOXYLASE	A, B, C, D	563	Kluyveromyces lactis	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.230 (Depositor), 0.229 (DCC)
R-Value Work: 0.178 (Depositor), 0.177 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.709	α = 90
b = 203.175	β = 91.81
c = 79.815	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-01-27

Deposition Author(s):

This entry supersedes: 2G1I

Revision History (Full details and data files)

Version 1.0: 2009-01-27
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-01-30
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2019-02-06
Changes: Data collection, Experimental preparation
Version 1.5: 2019-07-10
Changes: Data collection
Version 1.6: 2019-07-24
Changes: Data collection
Version 1.7: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description