PDB entry 6kdy

View 6kdy on RCSB PDB site
Description: Crystal structure of the alpha bata heterodimer of human IDH3 in complex with NAD.
Class: oxidoreductase
Keywords: NAD dependent isocitrate dehydrogenase, OXIDOREDUCTASE
Deposited on 2019-07-03, released 2019-09-25
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-12-25, with a file datestamp of 2019-12-20.
Experiment type: XRAY
Resolution: 3.02 Å
R-factor: N/A
AEROSPACI score: 0.12 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH3A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6kdya_
  • Chain 'B':
    Compound: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH3B
    Database cross-references and differences (RAF-indexed):
    • Uniprot O43837 (Start-339)
      • expression tag (340-353)
    Domains in SCOPe 2.08: d6kdyb1, d6kdyb2
  • Chain 'C':
    Compound: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH3A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6kdyc_
  • Chain 'D':
    Compound: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH3B
    Database cross-references and differences (RAF-indexed):
    • Uniprot O43837 (Start-339)
      • expression tag (340-353)
    Domains in SCOPe 2.08: d6kdyd1, d6kdyd2
  • Chain 'E':
    Compound: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH3A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6kdye_
  • Chain 'F':
    Compound: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH3B
    Database cross-references and differences (RAF-indexed):
    • Uniprot O43837 (Start-339)
      • expression tag (340-353)
    Domains in SCOPe 2.08: d6kdyf1, d6kdyf2
  • Chain 'G':
    Compound: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH3A
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6kdyg_
  • Chain 'H':
    Compound: Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH3B
    Database cross-references and differences (RAF-indexed):
    • Uniprot O43837 (Start-339)
      • expression tag (340-353)
    Domains in SCOPe 2.08: d6kdyh1, d6kdyh2
  • Heterogens: NAD, PG4, 2PE, PE7, P6G

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6kdyA (A:)
gstggvqtvtlipgdgigpeisaavmkifdaakapiqweernvtaiqgpggkwmipseak
esmdknkmglkgplktpiaaghpsmnlllrktfdlyanvrpcvsiegyktpytdvnivti
rentegeysgiehvivdgvvqsiklitegaskriaefafeyarnnhrsnvtavhkanimr
msdglflqkcrevaesckdikfnemyldtvclnmvqdpsqfdvlvmpnlygdilsdlcag
ligglgvtpsgnigangvaifesvhgtapdiagkdmanptalllsavmmlrhmglfdhaa
rieaacfatikdgksltkdlggnakcsdfteeicrrvkdld

    Sequence, based on observed residues (ATOM records): (download) 
    >6kdyA (A:)
gvqtvtlipgdgigpeisaavmkifdaakapiqweernvtaiqgpggkwmipseakesmd
knkmglkgplktpiaaghpsmnlllrktfdlyanvrpcvsiegyktpytdvnivtirent
egeysgiehvivdgvvqsiklitegaskriaefafeyarnnhrsnvtavhkanimrmsdg
lflqkcrevaesckdikfnemyldtvclnmvqdpsqfdvlvmpnlygdilsdlcagligg
lgvtpsgnigangvaifesvhgtapdiagkdmanptalllsavmmlrhmglfdhaariea
acfatikdgksltkdlggnakcsdfteeicrrvkd

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6kdyB (B:)
asrsqaedvrvegsfpvtmlpgdgvgpelmhavkevfkaaavpvefqehhlsevqnmase
ekleqvlssmkenkvaiigkihtpmeykgelasydmrlrrkldlfanvvhvkslpgymtr
hnnldlviireqtegeysslehesargvieclkivtraksqriakfafdyatkkgrgkvt
avhkanimklgdglflqcceevaelypkikfetmiidnccmqlvqnpyqfdvlvmpnlyg
niidnlaaglvggagvvpgesysaeyavfetgarhpfaqavgrnianptamllsasnmlr
hlnleyhssmiadavkkvikvgkvrtsdmggyatchdfteeicrrvkdldenlyfq

    Sequence, based on observed residues (ATOM records): (download) 
    >6kdyB (B:)
sfpvtmlpgdgvgpelmhavkevfkaaavpvefqehhlsevqnmaseekleqvlssmken
kvaiigkihtpmeykgelasydmrlrrkldlfanvvhvkslpgymtrhnnldlviireqt
egeysslehesargvieclkivtraksqriakfafdyatkkgrgkvtavhkanimklgdg
lflqcceevaelypkikfetmiidnccmqlvqnpyqfdvlvmpnlygniidnlaaglvgg
agvvpgesysaeyavfetgarhpfaqavgrnianptamllsasnmlrhlnleyhssmiad
avkkvikvgkvrtsdmggyatchdfteeicrrvkdldenly

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6kdyC (C:)
gstggvqtvtlipgdgigpeisaavmkifdaakapiqweernvtaiqgpggkwmipseak
esmdknkmglkgplktpiaaghpsmnlllrktfdlyanvrpcvsiegyktpytdvnivti
rentegeysgiehvivdgvvqsiklitegaskriaefafeyarnnhrsnvtavhkanimr
msdglflqkcrevaesckdikfnemyldtvclnmvqdpsqfdvlvmpnlygdilsdlcag
ligglgvtpsgnigangvaifesvhgtapdiagkdmanptalllsavmmlrhmglfdhaa
rieaacfatikdgksltkdlggnakcsdfteeicrrvkdld

    Sequence, based on observed residues (ATOM records): (download) 
    >6kdyC (C:)
gvqtvtlipgdgigpeisaavmkifdaakapiqweernvtaiqgpggkwmipseakesmd
knkmglkgplktpiaaghpsmnlllrktfdlyanvrpcvsiegyktpytdvnivtirent
egeysgiehvivdgvvqsiklitegaskriaefafeyarnnhrsnvtavhkanimrmsdg
lflqkcrevaesckdikfnemyldtvclnmvqdpsqfdvlvmpnlygdilsdlcagligg
lgvtpsgnigangvaifesvhgtapdiagkdmanptalllsavmmlrhmglfdhaariea
acfatikdgksltkdlggnakcsdfteeicrrvkd

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6kdyD (D:)
asrsqaedvrvegsfpvtmlpgdgvgpelmhavkevfkaaavpvefqehhlsevqnmase
ekleqvlssmkenkvaiigkihtpmeykgelasydmrlrrkldlfanvvhvkslpgymtr
hnnldlviireqtegeysslehesargvieclkivtraksqriakfafdyatkkgrgkvt
avhkanimklgdglflqcceevaelypkikfetmiidnccmqlvqnpyqfdvlvmpnlyg
niidnlaaglvggagvvpgesysaeyavfetgarhpfaqavgrnianptamllsasnmlr
hlnleyhssmiadavkkvikvgkvrtsdmggyatchdfteeicrrvkdldenlyfq

    Sequence, based on observed residues (ATOM records): (download) 
    >6kdyD (D:)
gsfpvtmlpgdgvgpelmhavkevfkaaavpvefqehhlsevqnmaseekleqvlssmke
nkvaiigkihtpmeykgelasydmrlrrkldlfanvvhvkslpgymtrhnnldlviireq
tegeysslehesargvieclkivtraksqriakfafdyatkkgrgkvtavhkanimklgd
glflqcceevaelypkikfetmiidnccmqlvqnpyqfdvlvmpnlygniidnlaaglvg
gagvvpgesysaeyavfetgarhpfaqavgrnianptamllsasnmlrhlnleyhssmia
davkkvikvgkvrtsdmggyatchdfteeicrrvkdldenly

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >6kdyE (E:)
gstggvqtvtlipgdgigpeisaavmkifdaakapiqweernvtaiqgpggkwmipseak
esmdknkmglkgplktpiaaghpsmnlllrktfdlyanvrpcvsiegyktpytdvnivti
rentegeysgiehvivdgvvqsiklitegaskriaefafeyarnnhrsnvtavhkanimr
msdglflqkcrevaesckdikfnemyldtvclnmvqdpsqfdvlvmpnlygdilsdlcag
ligglgvtpsgnigangvaifesvhgtapdiagkdmanptalllsavmmlrhmglfdhaa
rieaacfatikdgksltkdlggnakcsdfteeicrrvkdld

    Sequence, based on observed residues (ATOM records): (download) 
    >6kdyE (E:)
vqtvtlipgdgigpeisaavmkifdaakapiqweernvtawmipseakesmdknkmglkg
plktpiaaghpsmnlllrktfdlyanvrpcvsiegyktpytdvnivtirentegeysgie
hvivdgvvqsiklitegaskriaefafeyarnnhrsnvtavhkanimrmsdglflqkcre
vaesckdikfnemyldtvclnmvqdpsqfdvlvmpnlygdilsdlcagligglgvtpsgn
igangvaifesvhgtapdiagkdmanptalllsavmmlrhmglfdhaarieaacfatikd
gksltkdlggnakcsdfteeicrrvkd

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >6kdyF (F:)
asrsqaedvrvegsfpvtmlpgdgvgpelmhavkevfkaaavpvefqehhlsevqnmase
ekleqvlssmkenkvaiigkihtpmeykgelasydmrlrrkldlfanvvhvkslpgymtr
hnnldlviireqtegeysslehesargvieclkivtraksqriakfafdyatkkgrgkvt
avhkanimklgdglflqcceevaelypkikfetmiidnccmqlvqnpyqfdvlvmpnlyg
niidnlaaglvggagvvpgesysaeyavfetgarhpfaqavgrnianptamllsasnmlr
hlnleyhssmiadavkkvikvgkvrtsdmggyatchdfteeicrrvkdldenlyfq

    Sequence, based on observed residues (ATOM records): (download) 
    >6kdyF (F:)
sfpvtmlpgdgvgpelmhavkevfkaaavpvefqehhlsevqnmaseekleqvlssmken
kvaiigkihtpmeykgelasydmrlrrkldlfanvvhvkslpgymtrhnnldlviireqt
egeysslehesargvieclkivtraksqriakfafdyatkkgrgkvtavhkanimklgdg
lflqcceevaelypkikfetmiidnccmqlvqnpyqfdvlvmpnlygniidnlaaglvgg
agvvpgesysaeyavfetgarhpfaqavgrnianptamllsasnmlrhlnleyhssmiad
avkkvikvgkvrtsdmggyatchdfteeicrrvkdldenly

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >6kdyG (G:)
gstggvqtvtlipgdgigpeisaavmkifdaakapiqweernvtaiqgpggkwmipseak
esmdknkmglkgplktpiaaghpsmnlllrktfdlyanvrpcvsiegyktpytdvnivti
rentegeysgiehvivdgvvqsiklitegaskriaefafeyarnnhrsnvtavhkanimr
msdglflqkcrevaesckdikfnemyldtvclnmvqdpsqfdvlvmpnlygdilsdlcag
ligglgvtpsgnigangvaifesvhgtapdiagkdmanptalllsavmmlrhmglfdhaa
rieaacfatikdgksltkdlggnakcsdfteeicrrvkdld

    Sequence, based on observed residues (ATOM records): (download) 
    >6kdyG (G:)
gvqtvtlipgdgigpeisaavmkifdaakapiqweernvtaiqgpggkwmipseakesmd
knkmglkgplktpiaaghpsmnlllrktfdlyanvrpcvsiegyktpytdvnivtirent
egeysgiehvivdgvvqsiklitegaskriaefafeyarnnhrsnvtavhkanimrmsdg
lflqkcrevaesckdikfnemyldtvclnmvqdpsqfdvlvmpnlygdilsdlcagligg
lgvtpsgnigangvaifesvhgtapdiagkdmanptalllsavmmlrhmglfdhaariea
acfatikdgksltkdlggnakcsdfteeicrrvkd

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >6kdyH (H:)
asrsqaedvrvegsfpvtmlpgdgvgpelmhavkevfkaaavpvefqehhlsevqnmase
ekleqvlssmkenkvaiigkihtpmeykgelasydmrlrrkldlfanvvhvkslpgymtr
hnnldlviireqtegeysslehesargvieclkivtraksqriakfafdyatkkgrgkvt
avhkanimklgdglflqcceevaelypkikfetmiidnccmqlvqnpyqfdvlvmpnlyg
niidnlaaglvggagvvpgesysaeyavfetgarhpfaqavgrnianptamllsasnmlr
hlnleyhssmiadavkkvikvgkvrtsdmggyatchdfteeicrrvkdldenlyfq

    Sequence, based on observed residues (ATOM records): (download) 
    >6kdyH (H:)
sfpvtmlpgdgvgpelmhavkevfkaaavpvefqehhlsevqnmaseekleqvlssmken
kvaiigkihtpmeykgelasydmrlrrkldlfanvvhvkslpgymtrhnnldlviireqt
egeysslehesargvieclkivtraksqriakfafdyatkkgrgkvtavhkanimklgdg
lflqcceevaelypkikfetmiidnccmqlvqnpyqfdvlvmpnlygniidnlaaglvgg
agvvpgesysaeyavfetgarhpfaqavgrnianptamllsasnmlrhlnleyhssmiad
avkkvikvgkvrtsdmggyatchdfteeicrrvkdldenly