PDB entry 2vjy

View 2vjy on RCSB PDB site
Description: pyruvate decarboxylase from kluyveromyces lactis in complex with the substrate analogue methyl acetylphosphonate
Class: lyase
Keywords: metal-binding, decarboxylase, dimer of dimers, methylacetylphosphonate, methyl acetylphosphonate, substrate activation, thiamine diphosphate, thiamine pyrophosphate, asymmetric active sites, map, lyase, pyruvate, magnesium, flavoprotein
Deposited on 2007-12-14, released 2009-01-27
The last revision prior to the SCOPe 2.07 freeze date was dated 2009-05-05, with a file datestamp of 2009-05-01.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: 0.154
AEROSPACI score: 0.39 (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 2.07: d2vjya1, d2vjya2, d2vjya3
  • Chain 'B':
    Compound: pyruvate decarboxylase
    Species: Kluyveromyces lactis [TaxId:28985]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2vjyb1, d2vjyb2, d2vjyb3
  • Chain 'C':
    Compound: pyruvate decarboxylase
    Species: Kluyveromyces lactis [TaxId:28985]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2vjyc1, d2vjyc2, d2vjyc3
  • Chain 'D':
    Compound: pyruvate decarboxylase
    Species: Kluyveromyces lactis [TaxId:28985]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2vjyd1, d2vjyd2, d2vjyd3
  • Heterogens: TPP, MG, ALK, ALU, HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download)
    >2vjyA (A:)
    seitlgrylferlkqvevqtifglpgdfnlslldniyevpgmrwagnanelnaayaadgy
    arlkgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsvssqakqlllhhtlgngd
    ftvfhrmssnisettamitdintapaeidrcirttyvsqrpvylglpanlvdltvpasll
    dtpidlslkpndpeaeeevienvlqlikeaknpviladaccsrhdakaetkklidltqfp
    afvtpmgkgsidekhprfggvyvgtlsspavkeavesadlvlsvgallsdfntgsfsysy
    ktknivefhsdytkirsatfpgvqmkfalqklltkvadaakgykpvpvpsepehneavad
    stplkqewvwtqvgeflregdvvitetgtsafginqthfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytierlih
    getaqynciqnwqhlellptfgakdyeavrvsttgewnklttdekfqdntrirlievmlp
    tmdapsnlvkqaqltaatnakn
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >2vjyB (B:)
    seitlgrylferlkqvevqtifglpgdfnlslldniyevpgmrwagnanelnaayaadgy
    arlkgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsvssqakqlllhhtlgngd
    ftvfhrmssnisettamitdintapaeidrcirttyvsqrpvylglpanlvdltvpasll
    dtpidlslkpndpeaeeevienvlqlikeaknpviladaccsrhdakaetkklidltqfp
    afvtpmgkgsidekhprfggvyvgtlsspavkeavesadlvlsvgallsdfntgsfsysy
    ktknivefhsdytkirsatfpgvqmkfalqklltkvadaakgykpvpvpsepehneavad
    stplkqewvwtqvgeflregdvvitetgtsafginqthfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytierlih
    getaqynciqnwqhlellptfgakdyeavrvsttgewnklttdekfqdntrirlievmlp
    tmdapsnlvkqaqltaatnakn
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >2vjyC (C:)
    seitlgrylferlkqvevqtifglpgdfnlslldniyevpgmrwagnanelnaayaadgy
    arlkgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsvssqakqlllhhtlgngd
    ftvfhrmssnisettamitdintapaeidrcirttyvsqrpvylglpanlvdltvpasll
    dtpidlslkpndpeaeeevienvlqlikeaknpviladaccsrhdakaetkklidltqfp
    afvtpmgkgsidekhprfggvyvgtlsspavkeavesadlvlsvgallsdfntgsfsysy
    ktknivefhsdytkirsatfpgvqmkfalqklltkvadaakgykpvpvpsepehneavad
    stplkqewvwtqvgeflregdvvitetgtsafginqthfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytierlih
    getaqynciqnwqhlellptfgakdyeavrvsttgewnklttdekfqdntrirlievmlp
    tmdapsnlvkqaqltaatnakn
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >2vjyD (D:)
    seitlgrylferlkqvevqtifglpgdfnlslldniyevpgmrwagnanelnaayaadgy
    arlkgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsvssqakqlllhhtlgngd
    ftvfhrmssnisettamitdintapaeidrcirttyvsqrpvylglpanlvdltvpasll
    dtpidlslkpndpeaeeevienvlqlikeaknpviladaccsrhdakaetkklidltqfp
    afvtpmgkgsidekhprfggvyvgtlsspavkeavesadlvlsvgallsdfntgsfsysy
    ktknivefhsdytkirsatfpgvqmkfalqklltkvadaakgykpvpvpsepehneavad
    stplkqewvwtqvgeflregdvvitetgtsafginqthfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytierlih
    getaqynciqnwqhlellptfgakdyeavrvsttgewnklttdekfqdntrirlievmlp
    tmdapsnlvkqaqltaatnakn