PDB entry 1yba

View 1yba on RCSB PDB site
Description: The active form of phosphoglycerate dehydrogenase
Class: oxidoreductase
Keywords: oxidoreductase
Deposited on 2004-12-20, released 2005-04-26
The last revision prior to the SCOPe 2.06 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 2.24 Å
R-factor: 0.189
AEROSPACI score: 0.37 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: D-3-phosphoglycerate dehydrogenase
    Species: Escherichia coli [TaxId:562]
    Gene: serA
    Database cross-references and differences (RAF-indexed):
    • Uniprot P08328 (Start-409)
      • modified residue (174)
      • modified residue (202)
      • modified residue (219-220)
      • modified residue (228)
      • modified residue (340)
      • modified residue (375)
      • modified residue (396)
    Domains in SCOPe 2.06: d1ybaa1, d1ybaa2, d1ybaa3
  • Chain 'B':
    Compound: D-3-phosphoglycerate dehydrogenase
    Species: Escherichia coli [TaxId:562]
    Gene: serA
    Database cross-references and differences (RAF-indexed):
    • Uniprot P08328 (Start-409)
      • modified residue (174)
      • modified residue (202)
      • modified residue (219-220)
      • modified residue (228)
      • modified residue (340)
      • modified residue (375)
      • modified residue (396)
    Domains in SCOPe 2.06: d1ybab1, d1ybab2, d1ybab3
  • Chain 'C':
    Compound: D-3-phosphoglycerate dehydrogenase
    Species: Escherichia coli [TaxId:562]
    Gene: serA
    Database cross-references and differences (RAF-indexed):
    • Uniprot P08328 (Start-409)
      • modified residue (174)
      • modified residue (202)
      • modified residue (219-220)
      • modified residue (228)
      • modified residue (340)
      • modified residue (375)
      • modified residue (396)
    Domains in SCOPe 2.06: d1ybac1, d1ybac2, d1ybac3
  • Chain 'D':
    Compound: D-3-phosphoglycerate dehydrogenase
    Species: Escherichia coli [TaxId:562]
    Gene: serA
    Database cross-references and differences (RAF-indexed):
    • Uniprot P08328 (Start-409)
      • modified residue (174)
      • modified residue (202)
      • modified residue (219-220)
      • modified residue (228)
      • modified residue (340)
      • modified residue (375)
      • modified residue (396)
    Domains in SCOPe 2.06: d1ybad1, d1ybad2, d1ybad3
  • Heterogens: PO4, AKG, UNL, NAD, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >1ybaA (A:)
    makvslekdkikfllvegvhqkaleslraagytniefhkgalddeqlkesirdahfiglr
    srthltedvinaaeklvaigcfcigtnqvdldaaakrgipvfnapfsntrsvaelvigel
    llllrgvpeanakahrgvwnklaagsfeargkklgiigyghigtqlgilaeslgmyvyfy
    dienklplgnatqvqhlsdllnmsdvvslhvpenpstknmmgakeislmkpgsllinasr
    gtvvdipalcdalaskhlagaaidvfptepatnsdpftsplcefdnvlltphiggstqea
    qeniglevagklikysdngstlsavnfpevslplhggrrlmhihenrpgvltalnkifae
    qgvniaaqylqtsaqmgyvvidieadedvaekalqamkaipgtirarlly
    

    Sequence, based on observed residues (ATOM records): (download)
    >1ybaA (A:)
    slekdkikfllvegvhqkaleslraagytniefhkgalddeqlkesirdahfiglrsrth
    ltedvinaaeklvaigcfcigtnqvdldaaakrgipvfnapfsntrsvaelvigelllll
    rgvpeanakahrgvwnklaagsfeargkklgiigyghigtqlgilaeslgmyvyfydien
    klplgnatqvqhlsdllnmsdvvslhvpenpstknmmgakeislmkpgsllinasrgtvv
    dipalcdalaskhlagaaidvfptepatnsdpftsplcefdnvlltphiggstqeaqeni
    glevagklikysdngstlsavnfpevslplhggrrlmhihenrpgvltalnkifaeqgvn
    iaaqylqtsaqmgyvvidieadedvaekalqamkaipgtirarlly
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >1ybaB (B:)
    makvslekdkikfllvegvhqkaleslraagytniefhkgalddeqlkesirdahfiglr
    srthltedvinaaeklvaigcfcigtnqvdldaaakrgipvfnapfsntrsvaelvigel
    llllrgvpeanakahrgvwnklaagsfeargkklgiigyghigtqlgilaeslgmyvyfy
    dienklplgnatqvqhlsdllnmsdvvslhvpenpstknmmgakeislmkpgsllinasr
    gtvvdipalcdalaskhlagaaidvfptepatnsdpftsplcefdnvlltphiggstqea
    qeniglevagklikysdngstlsavnfpevslplhggrrlmhihenrpgvltalnkifae
    qgvniaaqylqtsaqmgyvvidieadedvaekalqamkaipgtirarlly
    

    Sequence, based on observed residues (ATOM records): (download)
    >1ybaB (B:)
    slekdkikfllvegvhqkaleslraagytniefhkgalddeqlkesirdahfiglrsrth
    ltedvinaaeklvaigcfcigtnqvdldaaakrgipvfnapfsntrsvaelvigelllll
    rgvpeanakahrgvwnklaagsfeargkklgiigyghigtqlgilaeslgmyvyfydien
    klplgnatqvqhlsdllnmsdvvslhvpenpstknmmgakeislmkpgsllinasrgtvv
    dipalcdalaskhlagaaidvfptepatnsdpftsplcefdnvlltphiggstqeaqeni
    glevagklikysdngstlsavnfpevslplhggrrlmhihenrpgvltalnkifaeqgvn
    iaaqylqtsaqmgyvvidieadedvaekalqamkaipgtirarlly
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >1ybaC (C:)
    makvslekdkikfllvegvhqkaleslraagytniefhkgalddeqlkesirdahfiglr
    srthltedvinaaeklvaigcfcigtnqvdldaaakrgipvfnapfsntrsvaelvigel
    llllrgvpeanakahrgvwnklaagsfeargkklgiigyghigtqlgilaeslgmyvyfy
    dienklplgnatqvqhlsdllnmsdvvslhvpenpstknmmgakeislmkpgsllinasr
    gtvvdipalcdalaskhlagaaidvfptepatnsdpftsplcefdnvlltphiggstqea
    qeniglevagklikysdngstlsavnfpevslplhggrrlmhihenrpgvltalnkifae
    qgvniaaqylqtsaqmgyvvidieadedvaekalqamkaipgtirarlly
    

    Sequence, based on observed residues (ATOM records): (download)
    >1ybaC (C:)
    slekdkikfllvegvhqkaleslraagytniefhkgalddeqlkesirdahfiglrsrth
    ltedvinaaeklvaigcfcigtnqvdldaaakrgipvfnapfsntrsvaelvigelllll
    rgvpeanakahrgvwnklaagsfeargkklgiigyghigtqlgilaeslgmyvyfydien
    klplgnatqvqhlsdllnmsdvvslhvpenpstknmmgakeislmkpgsllinasrgtvv
    dipalcdalaskhlagaaidvfptepatnsdpftsplcefdnvlltphiggstqeaqeni
    glevagklikysdngstlsavnfpevslplhggrrlmhihenrpgvltalnkifaeqgvn
    iaaqylqtsaqmgyvvidieadedvaekalqamkaipgtirarlly
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >1ybaD (D:)
    makvslekdkikfllvegvhqkaleslraagytniefhkgalddeqlkesirdahfiglr
    srthltedvinaaeklvaigcfcigtnqvdldaaakrgipvfnapfsntrsvaelvigel
    llllrgvpeanakahrgvwnklaagsfeargkklgiigyghigtqlgilaeslgmyvyfy
    dienklplgnatqvqhlsdllnmsdvvslhvpenpstknmmgakeislmkpgsllinasr
    gtvvdipalcdalaskhlagaaidvfptepatnsdpftsplcefdnvlltphiggstqea
    qeniglevagklikysdngstlsavnfpevslplhggrrlmhihenrpgvltalnkifae
    qgvniaaqylqtsaqmgyvvidieadedvaekalqamkaipgtirarlly
    

    Sequence, based on observed residues (ATOM records): (download)
    >1ybaD (D:)
    slekdkikfllvegvhqkaleslraagytniefhkgalddeqlkesirdahfiglrsrth
    ltedvinaaeklvaigcfcigtnqvdldaaakrgipvfnapfsntrsvaelvigelllll
    rgvpeanakahrgvwnklaagsfeargkklgiigyghigtqlgilaeslgmyvyfydien
    klplgnatqvqhlsdllnmsdvvslhvpenpstknmmgakeislmkpgsllinasrgtvv
    dipalcdalaskhlagaaidvfptepatnsdpftsplcefdnvlltphiggstqeaqeni
    glevagklikysdngstlsavnfpevslplhggrrlmhihenrpgvltalnkifaeqgvn
    iaaqylqtsaqmgyvvidieadedvaekalqamkaipgtirarlly