1PED BACTERIAL SECONDARY ALCOHOL DEHYDROGENASE (APO-FORM) date
authors Korkhin, Y., Frolow, F.
compound source
symmetry
R_factor
R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.15
ligand ZN enzyme
related structures by homologous chain: 1KEV
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCrystalline alcohol dehydrogenases from the mesophilic bacterium Clostridium beijerinckii and the thermophilic bacterium Thermoanaerobium brockii: preparation, characterization and molecular symmetry., Korkhin Y, Frolow F, Bogin O, Peretz M, Kalb AJ, Burstein Y, Acta Crystallogr D Biol Crystallogr. 1996 Jul 1;52(Pt 4):882-6. PMID:15299659
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (231 Kb) [Save to disk]
  • Biological Unit Coordinates (1ped.pdb1.gz) 227 Kb
  • LPC: Ligand-Protein Contacts for 1PED
  • CSU: Contacts of Structural Units for 1PED
  • Likely Quarternary Molecular Structure file(s) for 1PED
  • Retrieve 1PED in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PED from S2C, [Save to disk]
    • View 1PED 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 1PED
  • 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 1PED, from MSDmotif at EBI
  • Genome occurence of 1PED's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1peda1, region A:1-139,A:314-351 [Jmol] [rasmolscript] [script source]
        - Domain d1peda2, region A:140-313 [Jmol] [rasmolscript] [script source]
        - Domain d1pedb1, region B:1-139,B:314-351 [Jmol] [rasmolscript] [script source]
        - Domain d1pedb2, region B:140-313 [Jmol] [rasmolscript] [script source]
        - Domain d1pedc1, region C:1-139,C:314-351 [Jmol] [rasmolscript] [script source]
        - Domain d1pedc2, region C:140-313 [Jmol] [rasmolscript] [script source]
        - Domain d1pedd1, region D:1-139,D:314-351 [Jmol] [rasmolscript] [script source]
        - Domain d1pedd2, region D:140-313 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ped 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: [1ped_D] [1ped_A] [1ped] [1ped_C] [1ped_B]
  • SWISS-PROT database: [P25984]
  • Domain organization of [ADH_CLOBE] by SWISSPFAM
    • Other resources with information on 1PED
  • Community annotation for 1PED 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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