1QPB Lyase date Nov 26, 1999
title Pyruvate Decarboyxlase From Yeast (Form B) Complexed With Py
authors G.Lu, D.Dobritzsch, G.Schneider
compound source
Molecule: Pyruvate Decarboxylase (Form B)
Chain: A, B
Synonym: Alpha-Carboxylase, Pyruvic Decarboxylase, Alpha-Ke Carboxylase;
Ec: 4.1.1.1
Other_details: Form B
Organism_scientific: Saccharomyces Pastorianus
Organism_taxid: 520522
Strain: Weihenstephan 3470 (2124, Bohemian Lager)
symmetry Space Group: C 1 2 1
R_factor 0.233 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
145.049 119.700 81.283 90.00 120.21 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand MG, PYM, TPP enzyme Lyase E.C.4.1.1.1 BRENDA
note 1QPB supersedes 1YPD
related structures by homologous chain: 1PYD
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe structural basis of substrate activation in yeast pyruvate decarboxylase. A crystallographic and kinetic study., Lu G, Dobritzsch D, Baumann S, Schneider G, Konig S, Eur J Biochem 2000 Feb;267(3):861-8. PMID:10651824
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (180 Kb) [Save to disk]
  • Biological Unit Coordinates (1qpb.pdb1.gz) 345 Kb
  • Biological Unit Coordinates (1qpb.pdb2.gz) 174 Kb
  • LPC: Ligand-Protein Contacts for 1QPB
  • CSU: Contacts of Structural Units for 1QPB
  • Likely Quarternary Molecular Structure file(s) for 1QPB
  • Structure Factors (337 Kb)
  • Retrieve 1QPB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QPB from S2C, [Save to disk]
  • Re-refined 1qpb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1QPB in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1QPB
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1QPB, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1qpba1, region A:182-360 [Jmol] [rasmolscript] [script source]
        - Domain d1qpba2, region A:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1qpba3, region A:361-556 [Jmol] [rasmolscript] [script source]
        - Domain d1qpbb1, region B:182-360 [Jmol] [rasmolscript] [script source]
        - Domain d1qpbb2, region B:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1qpbb3, region B:361-556 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1qpb_A] [1qpb] [1qpb_B]
  • SWISS-PROT database: [P06169]
  • Domain organization of [PDC1_YEAST] by SWISSPFAM
  • Other resources with information on 1QPB
  • Community annotation for 1QPB at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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