1PVD Lyase (Carbon-Carbon) date Apr 20, 1995
title Crystal Structure Of The Thiamin Diphosphate Dependent Enzym Decarboxylase From The Yeast Saccharomyces Cerevisiae At 2. Angstroms Resolution
authors W.Furey, P.Arjunan
compound source
Molecule: Pyruvate Decarboxylase
Chain: A, B
Ec: 4.1.1.1
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
symmetry Space Group: C 1 2 1
R_factor 0.165 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
142.060 74.750 120.320 90.00 116.58 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand MG, TPP enzyme Lyase E.C.4.1.1.1 BRENDA
related structures by homologous chain: 1PYD
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 A resolution., Arjunan P, Umland T, Dyda F, Swaminathan S, Furey W, Sax M, Farrenkopf B, Gao Y, Zhang D, Jordan F, J Mol Biol 1996 Mar 1;256(3):590-600. PMID:8604141
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (179 Kb) [Save to disk]
  • Biological Unit Coordinates (1pvd.pdb1.gz) 172 Kb
  • LPC: Ligand-Protein Contacts for 1PVD
  • CSU: Contacts of Structural Units for 1PVD
  • Likely Quarternary Molecular Structure file(s) for 1PVD
  • Structure Factors (642 Kb)
  • Retrieve 1PVD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PVD from S2C, [Save to disk]
  • Re-refined 1pvd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1PVD 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 1PVD
  • 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 1PVD, from MSDmotif at EBI
  • Genome occurence of 1PVD's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pvda1, region A:182-360 [Jmol] [rasmolscript] [script source]
        - Domain d1pvda2, region A:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1pvda3, region A:361-556 [Jmol] [rasmolscript] [script source]
        - Domain d1pvdb1, region B:182-360 [Jmol] [rasmolscript] [script source]
        - Domain d1pvdb2, region B:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1pvdb3, 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: [1pvd] [1pvd_B] [1pvd_A]
  • SWISS-PROT database: [P06169]
  • Domain organization of [PDC1_YEAST] by SWISSPFAM
    • Other resources with information on 1PVD
  • Community annotation for 1PVD 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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