PDB entry 5y4n

View 5y4n on RCSB PDB site
Description: Crystal structure of aerobically purified and anaerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase
Class: oxidoreductase
Keywords: [NiFe]-hydrogenase D. vulgaris, OXIDOREDUCTASE
Deposited on 2017-08-04, released 2018-08-08
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-08-08, with a file datestamp of 2018-08-03.
Experiment type: XRAY
Resolution: 1.69 Å
R-factor: N/A
AEROSPACI score: 0.41 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'L':
    Compound: Periplasmic [NiFe] hydrogenase Large subunit
    Species: Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637) [TaxId:883]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5y4nl_
  • Chain 'S':
    Compound: Periplasmic [NiFe] hydrogenase Small subunit
    Species: Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637) [TaxId:883]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5y4ns_
  • Heterogens: SF4, F3S, MPD, MRD, TRS, MG, NFU, HOH

PDB Chain Sequences:

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >5y4nL (L:)
    msgcraqnapggipvtpkssysgpivvdpvtrieghlrievevengkvknayssstlfrg
    leiilkgrdprdaqhftqrtcgvctythalastrcvdnavgvhipknatyirnlvlgaqy
    lhdhivhfyhlhaldfvdvtaalkadpakaakvassisprkttaadlkavqdklktfves
    gqlgpftnayflgghpayyldpetnliatahylealrlqvkaaramavfgaknphtqftv
    vggvtcydaltpqriaefealwketkafvdevyipdllvvaaaykdwtqyggtdnfitfg
    efpkdeydlnsrffkpgvvfkrdfknikpfdkmqieehvrhswyegaearhpwkgqtqpk
    ytdlhgddryswmkaprymgepmetgplaqvliaysqghpkvkavtdavlaklgvgpeal
    fstlgrtaargietaviaeyvgvmlqeykdniakgdnvicapwempkqaegvgfvnaprg
    glshwiriedgkignfqlvvpstwtlgprcdknklspveasligtpvadakrpveilrtv
    hsfdpciacgvh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5y4nL (L:)
    ssysgpivvdpvtrieghlrievevengkvknayssstlfrgleiilkgrdprdaqhftq
    rtcgvctythalastrcvdnavgvhipknatyirnlvlgaqylhdhivhfyhlhaldfvd
    vtaalkadpakaakvassisprkttaadlkavqdklktfvesgqlgpftnayflgghpay
    yldpetnliatahylealrlqvkaaramavfgaknphtqftvvggvtcydaltpqriaef
    ealwketkafvdevyipdllvvaaaykdwtqyggtdnfitfgefpkdeydlnsrffkpgv
    vfkrdfknikpfdkmqieehvrhswyegaearhpwkgqtqpkytdlhgddryswmkapry
    mgepmetgplaqvliaysqghpkvkavtdavlaklgvgpealfstlgrtaargietavia
    eyvgvmlqeykdniakgdnvicapwempkqaegvgfvnaprgglshwiriedgkignfql
    vvpstwtlgprcdknklspveasligtpvadakrpveilrtvhsfdpciacgvh
    

  • Chain 'S':
    Sequence, based on SEQRES records: (download)
    >5y4nS (S:)
    lmgprrpsvvylhnaectgcsesvlrafepyidtlildtlsldyhetimaaagdaaeaal
    eqavnsphgfiavveggiptaangiygkvanhtmldicsrilpkaqaviaygtcatfggv
    qaakpnptgakgvndalkhlgvkainiagcppnpynlvgtivyylknkaapeldslnrpt
    mffgqtvheqcprlphfdagefapsfeseearkgwclyelgckgpvtmnncpkikfnqtn
    wpvdaghpcigcsepdfwdamtpfyqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >5y4nS (S:)
    prrpsvvylhnaectgcsesvlrafepyidtlildtlsldyhetimaaagdaaeaaleqa
    vnsphgfiavveggiptaangiygkvanhtmldicsrilpkaqaviaygtcatfggvqaa
    kpnptgakgvndalkhlgvkainiagcppnpynlvgtivyylknkaapeldslnrptmff
    gqtvheqcprlphfdagefapsfeseearkgwclyelgckgpvtmnncpkikfnqtnwpv
    daghpcigcsepdfwdamtpfyqn