2PDA CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS AND PYRUVATE. date
authors Chabriere, E., Charon, M.H.
compound source
symmetry
R_factor
R_Free 0.297
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.00
ligand CA, MG, PYR, SF4, TPP enzyme
related structures by homologous chain: 1B0P
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • pyruvate synthase activity


    • Primary referenceCrystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate., Chabriere E, Charon MH, Volbeda A, Pieulle L, Hatchikian EC, Fontecilla-Camps JC, Nat Struct Biol 1999 Feb;6(2):182-90. PMID:10048931
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (383 Kb) [Save to disk]
  • Biological Unit Coordinates (2pda.pdb1.gz) 375 Kb
  • LPC: Ligand-Protein Contacts for 2PDA
  • CSU: Contacts of Structural Units for 2PDA
  • Likely Quarternary Molecular Structure file(s) for 2PDA
  • Retrieve 2PDA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PDA from S2C, [Save to disk]
    • View 2PDA 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 2PDA
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2PDA, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2pdaa1, region A:2-258 [Jmol] [rasmolscript] [script source]
        - Domain d2pdaa3, region A:259-415 [Jmol] [rasmolscript] [script source]
        - Domain d2pdaa4, region A:416-668 [Jmol] [rasmolscript] [script source]
        - Domain d2pdaa5, region A:669-785 [Jmol] [rasmolscript] [script source]
        - Domain d2pdaa2, region A:786-1232 [Jmol] [rasmolscript] [script source]
        - Domain d2pdab1, region B:2-258 [Jmol] [rasmolscript] [script source]
        - Domain d2pdab3, region B:259-415 [Jmol] [rasmolscript] [script source]
        - Domain d2pdab4, region B:416-668 [Jmol] [rasmolscript] [script source]
        - Domain d2pdab5, region B:669-785 [Jmol] [rasmolscript] [script source]
        - Domain d2pdab2, region B:786-1232 [Jmol] [rasmolscript] [script source]
  • Fold representative 2pda from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [2pda] [2pda_A] [2pda_B]
  • SWISS-PROT database: [P94692]
  • Domain organization of [P94692_DESAF] by SWISSPFAM
  • Domain found in 2PDA: [EKR ] by SMART
    • Other resources with information on 2PDA
  • Community annotation for 2PDA 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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