PDB entry 2vk4

View 2vk4 on RCSB PDB site
Description: crystal structure of pyruvate decarboxylase from kluyveromyces lactis
Class: lyase
Keywords: metal-binding, decarboxylase, dimer of dimers, substrate activation, thiamine diphosphate, tdp, tpp, lyase, magnesium, flavoprotein, thiamine pyrophosphate, asymmetric active sites
Deposited on 2007-12-17, released 2009-01-27
The last revision prior to the SCOPe 2.05 freeze date was dated 2009-01-27, with a file datestamp of 2009-02-03.
Experiment type: XRAY
Resolution: 1.95 Å
R-factor: 0.18
AEROSPACI score: 0.45 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: pyruvate decarboxylase
    Species: KLUYVEROMYCES LACTIS [TaxId:28985]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d2vk4a1, d2vk4a2, d2vk4a3
  • Chain 'B':
    Compound: pyruvate decarboxylase
    Species: KLUYVEROMYCES LACTIS [TaxId:28985]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d2vk4b1, d2vk4b2, d2vk4b3
  • Chain 'C':
    Compound: pyruvate decarboxylase
    Species: KLUYVEROMYCES LACTIS [TaxId:28985]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d2vk4c1, d2vk4c2, d2vk4c3
  • Chain 'D':
    Compound: pyruvate decarboxylase
    Species: KLUYVEROMYCES LACTIS [TaxId:28985]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d2vk4d1, d2vk4d2, d2vk4d3
  • Heterogens: TPP, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2vk4A (A:)
    mseitlgrylferlkqvevqtifglpgdfnlslldniyevpgmrwagnanelnaayaadg
    yarlkgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsvssqakqlllhhtlgng
    dftvfhrmssnisettamitdintapaeidrcirttyvsqrpvylglpanlvdltvpasl
    ldtpidlslkpndpeaeeevienvlqlikeaknpviladaccsrhdakaetkklidltqf
    pafvtpmgkgsidekhprfggvyvgtlsspavkeavesadlvlsvgallsdfntgsfsys
    yktknivefhsdytkirsatfpgvqmkfalqklltkvadaakgykpvpvpsepehneava
    dstplkqewvwtqvgeflregdvvitetgtsafginqthfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytierli
    hgetaqynciqnwqhlellptfgakdyeavrvsttgewnklttdekfqdntrirlievml
    ptmdapsnlvkqaqltaatnakn
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vk4A (A:)
    seitlgrylferlkqvevqtifglpgdfnlslldniyevpgmrwagnanelnaayaadgy
    arlkgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsvqakqlllhhtlgngdft
    vfhrmssnisettamitdintapaeidrcirttyvsqrpvylglpanlvdltvpaslldt
    pidlslkpndpeaeeevienvlqlikeaknpviladaccsrhdakaetkklidltqfpaf
    vtpmgkgsidekhprfggvyvgtlsspavkeavesadlvlsvgallsdfntgsfsysykt
    knivefhsdytkirsatfpgvqmkfalqklltkvadaakgykpvpvpsepehneavadst
    plkqewvwtqvgeflregdvvitetgtsafginqthfpnntygisqvlwgsigfttgatl
    gaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytierlihge
    taqynciqnwqhlellptfgakdyeavrvsttgewnklttdekfqdntrirlievmlptm
    dapsnlvkqaqltaatnakn
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2vk4B (B:)
    mseitlgrylferlkqvevqtifglpgdfnlslldniyevpgmrwagnanelnaayaadg
    yarlkgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsvssqakqlllhhtlgng
    dftvfhrmssnisettamitdintapaeidrcirttyvsqrpvylglpanlvdltvpasl
    ldtpidlslkpndpeaeeevienvlqlikeaknpviladaccsrhdakaetkklidltqf
    pafvtpmgkgsidekhprfggvyvgtlsspavkeavesadlvlsvgallsdfntgsfsys
    yktknivefhsdytkirsatfpgvqmkfalqklltkvadaakgykpvpvpsepehneava
    dstplkqewvwtqvgeflregdvvitetgtsafginqthfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytierli
    hgetaqynciqnwqhlellptfgakdyeavrvsttgewnklttdekfqdntrirlievml
    ptmdapsnlvkqaqltaatnakn
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vk4B (B:)
    seitlgrylferlkqvevqtifglpgdfnlslldniyevpgmrwagnanelnaayaadgy
    arlkgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsvssqallhhtlgngdftv
    fhrmssnisettamitdintapaeidrcirttyvsqrpvylglpanlvdltvpaslldtp
    idlslkpndpeaeeevienvlqlikeaknpviladaccsrhdakaetkklidltqfpafv
    tpmgkgsidekhprfggvyvgtlsspavkeavesadlvlsvgallsdfntgsfsysyktk
    nivefhsdytkirsatfpgvqmkfalqklltkvadaakgykpvpvpsepehneavadstp
    lkqewvwtqvgeflregdvvitetgtsafginqthfpnntygisqvlwgsigfttgatlg
    aafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytierlihget
    aqynciqnwqhlellptfgakdyeavrvsttgewnklttdekfqdntrirlievmlptmd
    apsnlvkqaqltaatna
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2vk4C (C:)
    mseitlgrylferlkqvevqtifglpgdfnlslldniyevpgmrwagnanelnaayaadg
    yarlkgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsvssqakqlllhhtlgng
    dftvfhrmssnisettamitdintapaeidrcirttyvsqrpvylglpanlvdltvpasl
    ldtpidlslkpndpeaeeevienvlqlikeaknpviladaccsrhdakaetkklidltqf
    pafvtpmgkgsidekhprfggvyvgtlsspavkeavesadlvlsvgallsdfntgsfsys
    yktknivefhsdytkirsatfpgvqmkfalqklltkvadaakgykpvpvpsepehneava
    dstplkqewvwtqvgeflregdvvitetgtsafginqthfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytierli
    hgetaqynciqnwqhlellptfgakdyeavrvsttgewnklttdekfqdntrirlievml
    ptmdapsnlvkqaqltaatnakn
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vk4C (C:)
    seitlgrylferlkqvevqtifglpgdfnlslldniyevpgmrwagnanelnaayaadgy
    arlkgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsakqlllhhtlgngdftvf
    hrmssnisettamitdintapaeidrcirttyvsqrpvylglpanlvdltvpaslldtpi
    dlslkpndpeaeeevienvlqlikeaknpviladaccsrhdakaetkklidltqfpafvt
    pmgkgsidekhprfggvyvgtlsspavkeavesadlvlsvgallsdfntgsfsysyktkn
    ivefhsdytkirsatfpgvqmkfalqklltkvadaakgykpvpvpsepehneavadstpl
    kqewvwtqvgeflregdvvitetgtsafginqthfpnntygisqvlwgsigfttgatlga
    afaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytierlihgeta
    qynciqnwqhlellptfgakdyeavrvsttgewnklttdekfqdntrirlievmlptmda
    psnlvkqaqltaatn
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2vk4D (D:)
    mseitlgrylferlkqvevqtifglpgdfnlslldniyevpgmrwagnanelnaayaadg
    yarlkgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsvssqakqlllhhtlgng
    dftvfhrmssnisettamitdintapaeidrcirttyvsqrpvylglpanlvdltvpasl
    ldtpidlslkpndpeaeeevienvlqlikeaknpviladaccsrhdakaetkklidltqf
    pafvtpmgkgsidekhprfggvyvgtlsspavkeavesadlvlsvgallsdfntgsfsys
    yktknivefhsdytkirsatfpgvqmkfalqklltkvadaakgykpvpvpsepehneava
    dstplkqewvwtqvgeflregdvvitetgtsafginqthfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytierli
    hgetaqynciqnwqhlellptfgakdyeavrvsttgewnklttdekfqdntrirlievml
    ptmdapsnlvkqaqltaatnakn
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vk4D (D:)
    seitlgrylferlkqvevqtifglpgdfnlslldniyevpgmrwagnanelnaayaadgy
    arlkgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsvqakqlllhhtlgngdft
    vfhrmssnisettamitdintapaeidrcirttyvsqrpvylglpanlvdltvpaslldt
    pidlslkpndpeaeeevienvlqlikeaknpviladaccsrhdakaetkklidltqfpaf
    vtpmgkgsidekhprfggvyvgtlsspavkeavesadlvlsvgallsdfntgsfsysykt
    knivefhsdytkirsatfpgvqmkfalqklltkvadaakgykpvpvpsepehneavadst
    plkqewvwtqvgeflregdvvitetgtsafginqthfpnntygisqvlwgsigfttgatl
    gaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytierlihge
    taqynciqnwqhlellptfgakdyeavrvsttgewnklttdekfqdntrirlievmlptm
    dapsnlvkqaqltaatnakn