PDB entry 2vk8

View 2vk8 on RCSB PDB site
Description: Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q 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 2007-12-17, released 2009-01-27
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-02-06, with a file datestamp of 2019-02-01.
Experiment type: XRAY
Resolution: 1.42 Å
R-factor: N/A
AEROSPACI score: 0.52 (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 (476)
      • conflict (205)
      • conflict (207)
      • conflict (537)
    Domains in SCOPe 2.08: d2vk8a1, d2vk8a2, d2vk8a3
  • 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 (476)
      • conflict (205)
      • conflict (207)
      • conflict (537)
    Domains in SCOPe 2.08: d2vk8b1, d2vk8b2, d2vk8b3
  • 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 (476)
      • conflict (205)
      • conflict (207)
      • conflict (537)
    Domains in SCOPe 2.08: d2vk8c1, d2vk8c2, d2vk8c3
  • 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 (476)
      • conflict (205)
      • conflict (207)
      • conflict (537)
    Domains in SCOPe 2.08: d2vk8d1, d2vk8d2, d2vk8d3
  • Heterogens: TPP, MG, 2OP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >2vk8A (A:)
mseitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadg
yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgng
dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
lqtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqf
pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
yktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavp
astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqkli
hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
pvfdapqnlveqakltaatnakq

    Sequence, based on observed residues (ATOM records): (download) 
    >2vk8A (A:)
seitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadgy
arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgngd
ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
qtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqfp
afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
ktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavpa
stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqklih
gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
vfdapqnlveqakltaatnakq

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >2vk8B (B:)
mseitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadg
yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgng
dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
lqtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqf
pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
yktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavp
astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqkli
hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
pvfdapqnlveqakltaatnakq

    Sequence, based on observed residues (ATOM records): (download) 
    >2vk8B (B:)
seitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadgy
arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgngd
ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
qtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqfp
afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
ktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavpa
stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqklih
gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
vfdapqnlveqakltaatnakq

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >2vk8C (C:)
mseitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadg
yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgng
dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
lqtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqf
pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
yktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavp
astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqkli
hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
pvfdapqnlveqakltaatnakq

    Sequence, based on observed residues (ATOM records): (download) 
    >2vk8C (C:)
seitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadgy
arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgngd
ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
qtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqfp
afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
ktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavpa
stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqklih
gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
vfdapqnlveqakltaatnakq

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >2vk8D (D:)
mseitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadg
yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgng
dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
lqtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqf
pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
yktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavp
astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqkli
hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
pvfdapqnlveqakltaatnakq

    Sequence, based on observed residues (ATOM records): (download) 
    >2vk8D (D:)
seitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadgy
arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgngd
ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
qtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqfp
afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
ktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavpa
stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqklih
gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
vfdapqnlveqakltaatnakq