PDB entry 2vk1

View 2vk1 on RCSB PDB site
Description: crystal structure of the saccharomyces cerevisiae pyruvate decarboxylase variant d28a in complex with its substrate
Class: lyase
Keywords: asymmetric active sites, phenylalanine catabolism, tryptophan catabolism, thiamine pyrophosphate, dimer of dimers, phosphorylation, allosteric enzyme, tdp, tpp, lyase, nucleus, pyruvate, cytoplasm, branched-chain amino acid catabolism, substrate activation, thiamine diphosphate, magnesium, acetylation, metal-binding, decarboxylase
Deposited on 2007-12-16, released 2009-01-27
The last revision prior to the SCOPe 2.06 freeze date was dated 2009-05-05, with a file datestamp of 2009-05-01.
Experiment type: XRAY
Resolution: 1.71 Å
R-factor: 0.191
AEROSPACI score: 0.53 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: pyruvate decarboxylase isozyme 1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06169 (Start-562)
      • engineered mutation (27)
    Domains in SCOPe 2.06: d2vk1a1, d2vk1a2, d2vk1a3
  • Chain 'B':
    Compound: pyruvate decarboxylase isozyme 1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06169 (Start-562)
      • engineered mutation (27)
    Domains in SCOPe 2.06: d2vk1b1, d2vk1b2, d2vk1b3
  • Chain 'C':
    Compound: pyruvate decarboxylase isozyme 1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06169 (Start-562)
      • engineered mutation (27)
    Domains in SCOPe 2.06: d2vk1c1, d2vk1c2, d2vk1c3
  • Chain 'D':
    Compound: pyruvate decarboxylase isozyme 1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06169 (Start-562)
      • engineered mutation (27)
    Domains in SCOPe 2.06: d2vk1d1, d2vk1d2, d2vk1d3
  • Heterogens: TPP, MG, PYR, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2vk1A (A:)
    mseitlgkylferlkqvnvntvfglpgafnlslldkiyevegmrwagnanelnaayaadg
    yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgng
    dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
    lqtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqf
    pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
    yktknivefhsdhmkirnatfpgvqmkfvlqklltaiadaakgykpvavpartpanaavp
    astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiekli
    hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
    pvfdapqnlveqakltaatnakq
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vk1A (A:)
    seitlgkylferlkqvnvntvfglpgafnlslldkiyevegmrwagnanelnaayaadgy
    arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgngd
    ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
    qtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqfp
    afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
    ktknivefhsdhmkirnatfpgvqmkfvlqklltaiadaakgykpvavpartpanaavpa
    stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytieklih
    gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
    vfdapqnlveqakltaatnakq
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2vk1B (B:)
    mseitlgkylferlkqvnvntvfglpgafnlslldkiyevegmrwagnanelnaayaadg
    yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgng
    dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
    lqtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqf
    pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
    yktknivefhsdhmkirnatfpgvqmkfvlqklltaiadaakgykpvavpartpanaavp
    astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiekli
    hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
    pvfdapqnlveqakltaatnakq
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vk1B (B:)
    seitlgkylferlkqvnvntvfglpgafnlslldkiyevegmrwagnanelnaayaadgy
    arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgngd
    ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
    qtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqfp
    afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
    ktknivefhsdhmkirnatfpgvqmkfvlqklltaiadaakgykpvavpartpanaavpa
    stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytieklih
    gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
    vfdapqnlveqakltaatnakq
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2vk1C (C:)
    mseitlgkylferlkqvnvntvfglpgafnlslldkiyevegmrwagnanelnaayaadg
    yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgng
    dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
    lqtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqf
    pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
    yktknivefhsdhmkirnatfpgvqmkfvlqklltaiadaakgykpvavpartpanaavp
    astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiekli
    hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
    pvfdapqnlveqakltaatnakq
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vk1C (C:)
    seitlgkylferlkqvnvntvfglpgafnlslldkiyevegmrwagnanelnaayaadgy
    arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgngd
    ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
    qtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqfp
    afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
    ktknivefhsdhmkirnatfpgvqmkfvlqklltaiadaakgykpvavpartpanaavpa
    stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytieklih
    gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
    vfdapqnlveqakltaatnakq
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2vk1D (D:)
    mseitlgkylferlkqvnvntvfglpgafnlslldkiyevegmrwagnanelnaayaadg
    yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgng
    dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
    lqtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqf
    pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
    yktknivefhsdhmkirnatfpgvqmkfvlqklltaiadaakgykpvavpartpanaavp
    astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiekli
    hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
    pvfdapqnlveqakltaatnakq
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vk1D (D:)
    seitlgkylferlkqvnvntvfglpgafnlslldkiyevegmrwagnanelnaayaadgy
    arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgngd
    ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
    qtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqfp
    afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
    ktknivefhsdhmkirnatfpgvqmkfvlqklltaiadaakgykpvavpartpanaavpa
    stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytieklih
    gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
    vfdapqnlveqakltaatnakq