PDB entry 6eo0

View 6eo0 on RCSB PDB site
Description: Zebrafish Sirt5 in complex with stalled peptidylimidate and bicyclic intermediate of inhibitory compound 29
Class: signaling protein
Keywords: Hydrolase, PTM, inhibitor, SIGNALING PROTEIN
Deposited on 2017-10-08, released 2017-11-01
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-11-22, with a file datestamp of 2017-11-17.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: N/A
AEROSPACI score: 0.22 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: NAD-dependent protein deacylase sirtuin-5, mitochondrial
    Species: Danio rerio [TaxId:7955]
    Gene: sirt5, si:ch211-121a2.1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q6DHI5 (6-276)
      • expression tag (3-5)
    Domains in SCOPe 2.07: d6eo0a1, d6eo0a2
  • Chain 'B':
    Compound: NAD-dependent protein deacylase sirtuin-5, mitochondrial
    Species: Danio rerio [TaxId:7955]
    Gene: sirt5, si:ch211-121a2.1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q6DHI5 (6-276)
      • expression tag (2-5)
    Domains in SCOPe 2.07: d6eo0b1, d6eo0b2
  • Chain 'C':
    Compound: NAD-dependent protein deacylase sirtuin-5, mitochondrial
    Species: Danio rerio [TaxId:7955]
    Gene: sirt5, si:ch211-121a2.1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q6DHI5 (6-276)
      • expression tag (3-5)
    Domains in SCOPe 2.07: d6eo0c1, d6eo0c2
  • Chain 'D':
    Compound: NAD-dependent protein deacylase sirtuin-5, mitochondrial
    Species: Danio rerio [TaxId:7955]
    Gene: sirt5, si:ch211-121a2.1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q6DHI5 (6-276)
      • expression tag (2-5)
    Domains in SCOPe 2.07: d6eo0d1, d6eo0d2
  • Heterogens: ZN, EDO, BV8, BVT, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6eo0A (A:)
    gidpftkmtrpssdltafrehfakakhiaiitgagvsaesgvptfrgpggfwrkwqaqdl
    atpeafsrdpslvwefyhyrrevmrskmpnpahlaiaecearlgqqgrsvviitqnidel
    hhragskhvyeihgslfktrcmscgevkanhkspicpaldgkgapdpntkearipvellp
    rcerkscngllrphvvwfgetldsdiltaverelekcdlclvvgtssivypaamfapqva
    srgvpvaefnmectpatqrfkyhfegpcgstlppale
    

    Sequence, based on observed residues (ATOM records): (download)
    >6eo0A (A:)
    pftkmtrpssdltafrehfakakhiaiitgagvsaesgvptfrgpggfwrkwqaqdlatp
    eafsrdpslvwefyhyrrevmrskmpnpahlaiaecearlgqqgrsvviitqnidelhhr
    agskhvyeihgslfktrcmscgevkanhkspicpaldgkgapdpntkearipvellprce
    rkscngllrphvvwfgetldsdiltaverelekcdlclvvgtssivypaamfapqvasrg
    vpvaefnmectpatqrfkyhfegpcgstlppale
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6eo0B (B:)
    gidpftkmtrpssdltafrehfakakhiaiitgagvsaesgvptfrgpggfwrkwqaqdl
    atpeafsrdpslvwefyhyrrevmrskmpnpahlaiaecearlgqqgrsvviitqnidel
    hhragskhvyeihgslfktrcmscgevkanhkspicpaldgkgapdpntkearipvellp
    rcerkscngllrphvvwfgetldsdiltaverelekcdlclvvgtssivypaamfapqva
    srgvpvaefnmectpatqrfkyhfegpcgstlppale
    

    Sequence, based on observed residues (ATOM records): (download)
    >6eo0B (B:)
    dpftkmtrpssdltafrehfakakhiaiitgagvsaesgvptfrgpggfwrkwqaqdlat
    peafsrdpslvwefyhyrrevmrskmpnpahlaiaecearlgqqgrsvviitqnidelhh
    ragskhvyeihgslfktrcmscgevkanhkspicpaldgkgapdpntkearipvellprc
    erkscngllrphvvwfgetldsdiltaverelekcdlclvvgtssivypaamfapqvasr
    gvpvaefnmectpatqrfkyhfegpcgstlppale
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6eo0C (C:)
    gidpftkmtrpssdltafrehfakakhiaiitgagvsaesgvptfrgpggfwrkwqaqdl
    atpeafsrdpslvwefyhyrrevmrskmpnpahlaiaecearlgqqgrsvviitqnidel
    hhragskhvyeihgslfktrcmscgevkanhkspicpaldgkgapdpntkearipvellp
    rcerkscngllrphvvwfgetldsdiltaverelekcdlclvvgtssivypaamfapqva
    srgvpvaefnmectpatqrfkyhfegpcgstlppale
    

    Sequence, based on observed residues (ATOM records): (download)
    >6eo0C (C:)
    pftkmtrpssdltafrehfakakhiaiitgagvsaesgvptfrgpggfwrkwqaqdlatp
    eafsrdpslvwefyhyrrevmrskmpnpahlaiaecearlgqqgrsvviitqnidelhhr
    agskhvyeihgslfktrcmscgevkanhkspicpaldgkgapdpntkearipvellprce
    rkscngllrphvvwfgetldsdiltaverelekcdlclvvgtssivypaamfapqvasrg
    vpvaefnmectpatqrfkyhfegpcgstlppale
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6eo0D (D:)
    gidpftkmtrpssdltafrehfakakhiaiitgagvsaesgvptfrgpggfwrkwqaqdl
    atpeafsrdpslvwefyhyrrevmrskmpnpahlaiaecearlgqqgrsvviitqnidel
    hhragskhvyeihgslfktrcmscgevkanhkspicpaldgkgapdpntkearipvellp
    rcerkscngllrphvvwfgetldsdiltaverelekcdlclvvgtssivypaamfapqva
    srgvpvaefnmectpatqrfkyhfegpcgstlppale
    

    Sequence, based on observed residues (ATOM records): (download)
    >6eo0D (D:)
    dpftkmtrpssdltafrehfakakhiaiitgagvsaesgvptfrgpggfwrkwqaqdlat
    peafsrdpslvwefyhyrrevmrskmpnpahlaiaecearlgqqgrsvviitqnidelhh
    ragskhvyeihgslfktrcmscgevkanhkspicpaldgkgapdpntkearipvellprc
    erkscngllrphvvwfgetldsdiltaverelekcdlclvvgtssivypaamfapqvasr
    gvpvaefnmectpatqrfkyhfegpcgstlppale