PDB entry 3daf

View 3daf on RCSB PDB site
Description: The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII cocrystallized with cyanide
Class: oxidoreductase
Keywords: ROSSMANN FOLD, HELIX BUNDLE, Methanogenesis, One-carbon metabolism, OXIDOREDUCTASE
Deposited on 2008-05-29, released 2008-12-09
The last revision prior to the SCOPe 2.07 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 1.75 Å
R-factor: 0.188
AEROSPACI score: 0.52 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 5,10-methenyltetrahydromethanopterin hydrogenase
    Species: Methanocaldococcus jannaschii [TaxId:2190]
    Gene: hmd, MJ0784
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q58194 (0-End)
      • conflict (338)
    Domains in SCOPe 2.07: d3dafa1, d3dafa2
  • Heterogens: PO4, FE2, CYN, CMO, FEG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3dafA (A:)
    mkiailgagcyrthaaagitnfmracevakevgkpeialthssitygaellhlvpdvkev
    ivsdpcfaeepglvvidefdpkevmeahlsgnpesimpkirevvkakakelpkppkacih
    lvhpedvglkvtsddreavegadivitwlpkgnkqpdiikkfadaipegaivthactipt
    tkfakifkdlgredlnitsyhpgcvpemkgqvyiaegyaseeavnklyeigkiargkafk
    mpanligpvcdmcsavtatvyagllayrdavtkilgapadfaqmmadealtqihnlmkek
    gianmeealdpaallgtadsmcfgplaeilptalkvlevhkvveeegktkceimsqke
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dafA (A:)
    mkiailgagcyrthaaagitnfmracevakevgkpeialthssitygaellhlvpdvkev
    ivsdpcfaeepglvvidefdpkevmeahlsgnpesimpkirevvkakakelpkppkacih
    lvhpedvglkvtsddreavegadivitwlpkgnkqpdiikkfadaipegaivthactipt
    tkfakifkdlgredlnitsyhpgcvpemkgqvyiaegyaseeavnklyeigkiargkafk
    mpanligpvcdmcsavtatvyagllayrdavtkilgapadfaqmmadealtqihnlmkek
    gianmeealdpaallgtadsmcfgplaeilptalkvlevhkvve