PDB entry 3duf

View 3duf on RCSB PDB site
Description: Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex
Class: oxidoreductase/transferase
Keywords: OXIDOREDUCTASE, PYRUVATE, DEHYDROGENASE, DIHYDROLIPOYL, ACETYL TRANSFERASE, MULTIENZYME COMPLEX, TRANSFERASE, Glycolysis, Phosphoprotein, Thiamine pyrophosphate, Acyltransferase, OXIDOREDUCTASE/TRANSFERASE COMPLEX
Deposited on 2008-07-17, released 2009-01-06
The last revision prior to the SCOPe 2.07 freeze date was dated 2009-01-06, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: 0.192
AEROSPACI score: 0.34 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Pyruvate dehydrogenase E1 component subunit alpha
    Species: Bacillus stearothermophilus
    Gene: pdhA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3dufa_
  • Chain 'B':
    Compound: Pyruvate dehydrogenase E1 component subunit beta
    Species: Bacillus stearothermophilus
    Gene: pdhB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3dufb1, d3dufb2
  • Chain 'C':
    Compound: Pyruvate dehydrogenase E1 component subunit alpha
    Species: Bacillus stearothermophilus
    Gene: pdhA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3dufc_
  • Chain 'D':
    Compound: Pyruvate dehydrogenase E1 component subunit beta
    Species: Bacillus stearothermophilus
    Gene: pdhB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3dufd1, d3dufd2
  • Chain 'E':
    Compound: Pyruvate dehydrogenase E1 component subunit alpha
    Species: Bacillus stearothermophilus
    Gene: pdhA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3dufe_
  • Chain 'F':
    Compound: Pyruvate dehydrogenase E1 component subunit beta
    Species: Bacillus stearothermophilus
    Gene: pdhB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3duff1, d3duff2
  • Chain 'G':
    Compound: Pyruvate dehydrogenase E1 component subunit alpha
    Species: Bacillus stearothermophilus
    Gene: pdhA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3dufg_
  • Chain 'H':
    Compound: Pyruvate dehydrogenase E1 component subunit beta
    Species: Bacillus stearothermophilus
    Gene: pdhB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3dufh1, d3dufh2
  • Chain 'I':
    Compound: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
    Species: Bacillus stearothermophilus
    Gene: pdhC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3dufi_
  • Chain 'J':
    Compound: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
    Species: Bacillus stearothermophilus
    Gene: pdhC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3dufj_
  • Heterogens: MG, K, R1T, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3dufA (A:)
    mgvktfqfpfaeqlekvaeqfptfqilneegevvneeampelsdeqlkelmrrmvytril
    dqrsislnrqgrlgfyaptagqeasqiashfalekedfilpgyrdvpqiiwhglplyqaf
    lfsrghfhgnqipegvnvlppqiiigaqyiqaagvalglkmrgkkavaitytgdggtsqg
    dfyeginfagafkapaifvvqnnrfaistpvekqtvaktlaqkavaagipgiqvdgmdpl
    avyaavkaareraingegptlietlcfrygphtmsgddptryrskelenewakkdplvrf
    rkfleakglwseeeennvieqakeeikeaikkadetpkqkvtdlisimfeelpfnlkeqy
    eiykekesk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dufA (A:)
    tfqfpfaeqlekvaeqfptfqilneegevvneeampelsdeqlkelmrrmvytrildqrs
    islnrqgrlgfyaptagqeasqiashfalekedfilpgyrdvpqiiwhglplyqaflfsr
    ghfhgnqipegvnvlppqiiigaqyiqaagvalglkmrgkkavaitytgdggtsqgdfye
    ginfagafkapaifvvqnnrfaistpvekqtvaktlaqkavaagipgiqvdgmdplavya
    avkaareraingegptlietlcfrygphtmsgddptryrskelenewakkdplvrfrkfl
    eakglwseeeennvieqakeeikeaikkadetpkqkvtdlisimfeelpfnlkeqyeiyk
    ekesk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3dufB (B:)
    maqmtmvqaitdalrielkndpnvlifgedvgvnggvfrateglqaefgedrvfdtplae
    sgigglaiglalqgfrpvpeiqffgfvyevmdsicgqmariryrtggryhmpitirspfg
    ggvhtpelhsdsleglvaqqpglkvvipstpydakgllisairdndpviflehlklyrsf
    rqevpegeytipigkadikregkditiiaygamvheslkaaaelekegisaevvdlrtvq
    pldietiigsvektgraivvqeaqrqagiaanvvaeinerailsleapvlrvaapdtvyp
    faqaesvwlpnfkdvietakkvmnf
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dufB (B:)
    aqmtmvqaitdalrielkndpnvlifgedvgvnggvfrateglqaefgedrvfdtplaes
    gigglaiglalqgfrpvpeiqffgfvyevmdsicgqmariryrtggryhmpitirspfgg
    gvhtpelhsdsleglvaqqpglkvvipstpydakgllisairdndpviflehlklyrsfr
    qevpegeytipigkadikregkditiiaygamvheslkaaaelekegisaevvdlrtvqp
    ldietiigsvektgraivvqeaqrqagiaanvvaeinerailsleapvlrvaapdtvypf
    aqaesvwlpnfkdvietakkvmnf
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3dufC (C:)
    mgvktfqfpfaeqlekvaeqfptfqilneegevvneeampelsdeqlkelmrrmvytril
    dqrsislnrqgrlgfyaptagqeasqiashfalekedfilpgyrdvpqiiwhglplyqaf
    lfsrghfhgnqipegvnvlppqiiigaqyiqaagvalglkmrgkkavaitytgdggtsqg
    dfyeginfagafkapaifvvqnnrfaistpvekqtvaktlaqkavaagipgiqvdgmdpl
    avyaavkaareraingegptlietlcfrygphtmsgddptryrskelenewakkdplvrf
    rkfleakglwseeeennvieqakeeikeaikkadetpkqkvtdlisimfeelpfnlkeqy
    eiykekesk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dufC (C:)
    tfqfpfaeqlekvaeqfptfqilneegevvneeampelsdeqlkelmrrmvytrildqrs
    islnrqgrlgfyaptagqeasqiashfalekedfilpgyrdvpqiiwhglplyqaflfsr
    ghfhgnqipegvnvlppqiiigaqyiqaagvalglkmrgkkavaitytgdggtsqgdfye
    ginfagafkapaifvvqnnrfaistpvekqtvaktlaqkavaagipgiqvdgmdplavya
    avkaareraingegptlietlcfrygphtmsgddptryrskelenewakkdplvrfrkfl
    eakglwseeeennvieqakeeikeaikkadetpkqkvtdlisimfeelpfnlkeqyeiyk
    ekesk
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3dufD (D:)
    maqmtmvqaitdalrielkndpnvlifgedvgvnggvfrateglqaefgedrvfdtplae
    sgigglaiglalqgfrpvpeiqffgfvyevmdsicgqmariryrtggryhmpitirspfg
    ggvhtpelhsdsleglvaqqpglkvvipstpydakgllisairdndpviflehlklyrsf
    rqevpegeytipigkadikregkditiiaygamvheslkaaaelekegisaevvdlrtvq
    pldietiigsvektgraivvqeaqrqagiaanvvaeinerailsleapvlrvaapdtvyp
    faqaesvwlpnfkdvietakkvmnf
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dufD (D:)
    aqmtmvqaitdalrielkndpnvlifgedvgvnggvfrateglqaefgedrvfdtplaes
    gigglaiglalqgfrpvpeiqffgfvyevmdsicgqmariryrtggryhmpitirspfgg
    gvhtpelhsdsleglvaqqpglkvvipstpydakgllisairdndpviflehlklyrsfr
    qevpegeytipigkadikregkditiiaygamvheslkaaaelekegisaevvdlrtvqp
    ldietiigsvektgraivvqeaqrqagiaanvvaeinerailsleapvlrvaapdtvypf
    aqaesvwlpnfkdvietakkvmnf
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3dufE (E:)
    mgvktfqfpfaeqlekvaeqfptfqilneegevvneeampelsdeqlkelmrrmvytril
    dqrsislnrqgrlgfyaptagqeasqiashfalekedfilpgyrdvpqiiwhglplyqaf
    lfsrghfhgnqipegvnvlppqiiigaqyiqaagvalglkmrgkkavaitytgdggtsqg
    dfyeginfagafkapaifvvqnnrfaistpvekqtvaktlaqkavaagipgiqvdgmdpl
    avyaavkaareraingegptlietlcfrygphtmsgddptryrskelenewakkdplvrf
    rkfleakglwseeeennvieqakeeikeaikkadetpkqkvtdlisimfeelpfnlkeqy
    eiykekesk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dufE (E:)
    tfqfpfaeqlekvaeqfptfqilneegevvneeampelsdeqlkelmrrmvytrildqrs
    islnrqgrlgfyaptagqeasqiashfalekedfilpgyrdvpqiiwhglplyqaflfsr
    ghfhgnqipegvnvlppqiiigaqyiqaagvalglkmrgkkavaitytgdggtsqgdfye
    ginfagafkapaifvvqnnrfaistpvekqtvaktlaqkavaagipgiqvdgmdplavya
    avkaareraingegptlietlcfrygphtmsgddptryrskelenewakkdplvrfrkfl
    eakglwseeeennvieqakeeikeaikkadetpkqkvtdlisimfeelpfnlkeqyeiyk
    ekesk
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3dufF (F:)
    maqmtmvqaitdalrielkndpnvlifgedvgvnggvfrateglqaefgedrvfdtplae
    sgigglaiglalqgfrpvpeiqffgfvyevmdsicgqmariryrtggryhmpitirspfg
    ggvhtpelhsdsleglvaqqpglkvvipstpydakgllisairdndpviflehlklyrsf
    rqevpegeytipigkadikregkditiiaygamvheslkaaaelekegisaevvdlrtvq
    pldietiigsvektgraivvqeaqrqagiaanvvaeinerailsleapvlrvaapdtvyp
    faqaesvwlpnfkdvietakkvmnf
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dufF (F:)
    aqmtmvqaitdalrielkndpnvlifgedvgvnggvfrateglqaefgedrvfdtplaes
    gigglaiglalqgfrpvpeiqffgfvyevmdsicgqmariryrtggryhmpitirspfgg
    gvhtpelhsdsleglvaqqpglkvvipstpydakgllisairdndpviflehlklyrsfr
    qevpegeytipigkadikregkditiiaygamvheslkaaaelekegisaevvdlrtvqp
    ldietiigsvektgraivvqeaqrqagiaanvvaeinerailsleapvlrvaapdtvypf
    aqaesvwlpnfkdvietakkvmnf
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3dufG (G:)
    mgvktfqfpfaeqlekvaeqfptfqilneegevvneeampelsdeqlkelmrrmvytril
    dqrsislnrqgrlgfyaptagqeasqiashfalekedfilpgyrdvpqiiwhglplyqaf
    lfsrghfhgnqipegvnvlppqiiigaqyiqaagvalglkmrgkkavaitytgdggtsqg
    dfyeginfagafkapaifvvqnnrfaistpvekqtvaktlaqkavaagipgiqvdgmdpl
    avyaavkaareraingegptlietlcfrygphtmsgddptryrskelenewakkdplvrf
    rkfleakglwseeeennvieqakeeikeaikkadetpkqkvtdlisimfeelpfnlkeqy
    eiykekesk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dufG (G:)
    tfqfpfaeqlekvaeqfptfqilneegevvneeampelsdeqlkelmrrmvytrildqrs
    islnrqgrlgfyaptagqeasqiashfalekedfilpgyrdvpqiiwhglplyqaflfsr
    ghfhgnqipegvnvlppqiiigaqyiqaagvalglkmrgkkavaitytgdggtsqgdfye
    ginfagafkapaifvvqnnrfaistpvekqtvaktlaqkavaagipgiqvdgmdplavya
    avkaareraingegptlietlcfrygphtmsgddptryrskelenewakkdplvrfrkfl
    eakglwseeeennvieqakeeikeaikkadetpkqkvtdlisimfeelpfnlkeqyeiyk
    ekesk
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3dufH (H:)
    maqmtmvqaitdalrielkndpnvlifgedvgvnggvfrateglqaefgedrvfdtplae
    sgigglaiglalqgfrpvpeiqffgfvyevmdsicgqmariryrtggryhmpitirspfg
    ggvhtpelhsdsleglvaqqpglkvvipstpydakgllisairdndpviflehlklyrsf
    rqevpegeytipigkadikregkditiiaygamvheslkaaaelekegisaevvdlrtvq
    pldietiigsvektgraivvqeaqrqagiaanvvaeinerailsleapvlrvaapdtvyp
    faqaesvwlpnfkdvietakkvmnf
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dufH (H:)
    aqmtmvqaitdalrielkndpnvlifgedvgvnggvfrateglqaefgedrvfdtplaes
    gigglaiglalqgfrpvpeiqffgfvyevmdsicgqmariryrtggryhmpitirspfgg
    gvhtpelhsdsleglvaqqpglkvvipstpydakgllisairdndpviflehlklyrsfr
    qevpegeytipigkadikregkditiiaygamvheslkaaaelekegisaevvdlrtvqp
    ldietiigsvektgraivvqeaqrqagiaanvvaeinerailsleapvlrvaapdtvypf
    aqaesvwlpnfkdvietakkvmnf
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >3dufI (I:)
    mafefklpdigegihegeivkwfvkpgdevneddvlcevqndkavveipspvkgkvleil
    vpegtvatvgqtlitldapgyenmtfkgqeqeeakkeektetvskeekvdavapnapaae
    aeagpnrrviampsvrkyarekgvdirlvqgtgkngrvlkedidaflaggakpapaaaee
    kaapaaakpattegefpetrekmsgirraiakamvhskhtaphvtlmdeadvtklvahrk
    kfkaiaaekgikltflpyvvkalvsalreypvlntsiddeteeiiqkhyynigiaadtdr
    gllvpvikhadrkpifalaqeinelaekardgkltpgemkgasctitnigsaggqwftpv
    inhpevailgigriaekpivrdgeivaapmlalslsfdhrmidgataqkalnhikrllsd
    pelllmea
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dufI (I:)
    rviampsvrkyarekgvdirlvqgtgkngrvlkedida
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >3dufJ (J:)
    mafefklpdigegihegeivkwfvkpgdevneddvlcevqndkavveipspvkgkvleil
    vpegtvatvgqtlitldapgyenmtfkgqeqeeakkeektetvskeekvdavapnapaae
    aeagpnrrviampsvrkyarekgvdirlvqgtgkngrvlkedidaflaggakpapaaaee
    kaapaaakpattegefpetrekmsgirraiakamvhskhtaphvtlmdeadvtklvahrk
    kfkaiaaekgikltflpyvvkalvsalreypvlntsiddeteeiiqkhyynigiaadtdr
    gllvpvikhadrkpifalaqeinelaekardgkltpgemkgasctitnigsaggqwftpv
    inhpevailgigriaekpivrdgeivaapmlalslsfdhrmidgataqkalnhikrllsd
    pelllmea
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dufJ (J:)
    iampsvrkyarekgvdirlvqgtgkngrvlkedida