PDB entry 3dva

View 3dva 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 2008-07-18, released 2009-01-13
The last revision prior to the SCOPe 2.07 freeze date was dated 2009-01-13, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.35 Å
R-factor: 0.192
AEROSPACI score: 0.38 (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):
    • Uniprot P21873 (Start-368)
      • engineered (206)
    Domains in SCOPe 2.07: d3dvaa_
  • 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: d3dvab1, d3dvab2
  • Chain 'C':
    Compound: Pyruvate dehydrogenase E1 component subunit alpha
    Species: Bacillus stearothermophilus
    Gene: pdhA
    Database cross-references and differences (RAF-indexed):
    • Uniprot P21873 (Start-368)
      • engineered (206)
    Domains in SCOPe 2.07: d3dvac_
  • 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: d3dvad1, d3dvad2
  • Chain 'E':
    Compound: Pyruvate dehydrogenase E1 component subunit alpha
    Species: Bacillus stearothermophilus
    Gene: pdhA
    Database cross-references and differences (RAF-indexed):
    • Uniprot P21873 (Start-368)
      • engineered (206)
    Domains in SCOPe 2.07: d3dvae_
  • 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: d3dvaf1, d3dvaf2
  • Chain 'G':
    Compound: Pyruvate dehydrogenase E1 component subunit alpha
    Species: Bacillus stearothermophilus
    Gene: pdhA
    Database cross-references and differences (RAF-indexed):
    • Uniprot P21873 (Start-368)
      • engineered (206)
    Domains in SCOPe 2.07: d3dvag_
  • 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: d3dvah1, d3dvah2
  • 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: d3dvai_
  • 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: d3dvaj_
  • Heterogens: MG, K, TPW, HOH

PDB Chain Sequences:

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

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

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

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

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

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

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

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

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

    Sequence, based on observed residues (ATOM records): (download) 
    >3dvaE (E:)
tfqfpfaeqlekvaeqfptfqilneegevvneeampelsdeqlkelmrrmvytrildqrs
islnrqgrlgfyaptagqeasqiashfalekedfilpgyrdvpqiiwhglplyqaflfsr
ghfhgnqipegvnvlppqiiigaqyiqaagvalglkmrgkkavaitytgdggtsqgdfye
ginfagafkapaifvvqnnrfaastpvekqtvaktlaqkavaagipgiqvdgmdplavya
avkaareraingegptlietlcfrygphtmsgdnewakkdplvrfrkfleakglwseeee
nnvieqakeeikeaikkadetpkqkvtdlisimfeelpfnlkeqyeiykekesk

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

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

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

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

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

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

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

    Sequence, based on observed residues (ATOM records): (download) 
    >3dvaI (I:)
rviampsvrkyarekgvdirlvqgtgkngrvlkedidaflag

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

    Sequence, based on observed residues (ATOM records): (download) 
    >3dvaJ (J:)
rviampsvrkyarekgvdirlvqgtgkngrvlkedidafl