PDB entry 2yid

View 2yid on RCSB PDB site
Description: crystal structure of the suca domain of mycobacterium smegmatis alpha-ketoglutarate decarboxylase in complex with the enamine-thdp intermediate
Deposited on 2011-05-11, released 2011-06-15
The last revision was dated 2011-10-12, with a file datestamp of 2011-10-07.
Experiment type: XRAY
Resolution: 2.25 Å
R-factor: 0.1935
AEROSPACI score: 0.39 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 2-oxoglutarate decarboxylase
    Species: MYCOBACTERIUM SMEGMATIS [TaxId:1772]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: 2-oxoglutarate decarboxylase
    Species: MYCOBACTERIUM SMEGMATIS [TaxId:1772]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: 2-oxoglutarate decarboxylase
    Species: MYCOBACTERIUM SMEGMATIS [TaxId:1772]
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: 2-oxoglutarate decarboxylase
    Species: MYCOBACTERIUM SMEGMATIS [TaxId:1772]
    Database cross-references and differences (RAF-indexed):
  • Heterogens: TD7, MG, CA, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >2yidA (A:)
    gdsiedknarvieliaayrnrghlmadidplrldntrfrshpdldvnshgltlwdldref
    kvdgfagvqrkklrdilsvlrdaycrhvgveythilepeqqrwiqervetkhdkptvaeq
    kyilsklnaaeafetflqtkyvgqkrfslegaetvipmmdavidqcaehgldevviamph
    rgrlnvlanivgkpysqifsefegnlnpsqahgsgdvkyhlgatgtyiqmfgdndievsl
    tanpshleavdpvleglvrakqdlldtgeegsdnrfsvvplmlhgdaafagqgvvaetln
    lallrgyrtggtihivvnnqigfttaptdsrsseyctdvakmigapifhvngddpeacaw
    varlavdfrqafkkdvvidmlcyrrrghnegddpsmtqpymydvidtkrgsrkayteali
    grgdismkeaedalrdyqgqlervfnevrelekheiepsesveadqqipsklatavdkam
    lqrigdahlalpegftvhprvrpvlekrremayegridwafaellalgsliaegklvrls
    gqdtqrgtftqrhavivdrktgeeftplqllatnpdgtptggkflvynsalsefaavgfe
    ygysvgnpdamvlweaqfgdfvngaqsiidefissgeakwgqlsdvvlllphghegqgpd
    htsgrierflqlwaegsmtiampstpanyfhllrrhgkdgiqrplivftpksmlrnkaav
    sdirdfteskfrsvleepmytdgegdrnkvtrllltsgkiyyelaarkakenredvaivr
    ieqlaplprrrlaetldrypnvkekfwvqeepanqgawpsfgltlpeilpdhftglkris
    rramsapssgsskvhaveqqeildtafg
    

    Sequence, based on observed residues (ATOM records):
    >2yidA (A:)
    dsiedknarvieliaayrnrghlmadidplrldntrltlwdldrefkvdvqrkklrdils
    vlrdaycrhvgveythilepeqqrwiqervetkhdkptvaeqkyilsklnaaeafetflq
    tkyvgqkrfslegaetvipmmdavidqcaehgldevviamphrgrlnvlanivgkpysqi
    fsefegnlnpsqahgsgdvkyhlgatgtyiqmfgdndievsltanpshleavdpvleglv
    rakqdlldtgeegsdnrfsvvplmlhgdaafagqgvvaetlnlallrgyrtggtihivvn
    nqigfttaptdsrsseyctdvakmigapifhvngddpeacawvarlavdfrqafkkdvvi
    dmlcyrrrghnegddpsmtqpymydvidtkrgsrkaytealigrgdismkeaedalrdyq
    gqlervfnevreleiepsesveadqqilatavdkamlqrigdahlalpegftvhprvrpv
    lekrremayegridwafaellalgsliaegklvrlsgqdtqrgtftqrhavivdrktgee
    ftplqllatnpdgtptggkflvynsalsefaavgfeygysvgnpdamvlweaqfgdfvng
    aqsiidefissgeakwgqlsdvvlllphghegqgpdhtsgrierflqlwaegsmtiamps
    tpanyfhllrrhgkdgiqrplivftpksmlrnkaavsdirdfteskfrsvleepmytdge
    gdrnkvtrllltsgkiyyelaarkakenredvaivrieqlaplprrrlaetldrypnvke
    kfwvqeepanqgawpsfgltlpeilpdhftglkrisrramsapssgsskvhaveqqeild
    tafg
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >2yidB (B:)
    gdsiedknarvieliaayrnrghlmadidplrldntrfrshpdldvnshgltlwdldref
    kvdgfagvqrkklrdilsvlrdaycrhvgveythilepeqqrwiqervetkhdkptvaeq
    kyilsklnaaeafetflqtkyvgqkrfslegaetvipmmdavidqcaehgldevviamph
    rgrlnvlanivgkpysqifsefegnlnpsqahgsgdvkyhlgatgtyiqmfgdndievsl
    tanpshleavdpvleglvrakqdlldtgeegsdnrfsvvplmlhgdaafagqgvvaetln
    lallrgyrtggtihivvnnqigfttaptdsrsseyctdvakmigapifhvngddpeacaw
    varlavdfrqafkkdvvidmlcyrrrghnegddpsmtqpymydvidtkrgsrkayteali
    grgdismkeaedalrdyqgqlervfnevrelekheiepsesveadqqipsklatavdkam
    lqrigdahlalpegftvhprvrpvlekrremayegridwafaellalgsliaegklvrls
    gqdtqrgtftqrhavivdrktgeeftplqllatnpdgtptggkflvynsalsefaavgfe
    ygysvgnpdamvlweaqfgdfvngaqsiidefissgeakwgqlsdvvlllphghegqgpd
    htsgrierflqlwaegsmtiampstpanyfhllrrhgkdgiqrplivftpksmlrnkaav
    sdirdfteskfrsvleepmytdgegdrnkvtrllltsgkiyyelaarkakenredvaivr
    ieqlaplprrrlaetldrypnvkekfwvqeepanqgawpsfgltlpeilpdhftglkris
    rramsapssgsskvhaveqqeildtafg
    

    Sequence, based on observed residues (ATOM records):
    >2yidB (B:)
    dknarvieliaayrnrghlmadidplrldwdldrefkvgvqrkklrdilsvlrdaycrhv
    gveythilepeqqrwiqervetkhdkptvaeqkyilsklnaaeafetflqtkyvgqkrfs
    legaetvipmmdavidqcaehgldevviamphrgrlnvlanivgkpysqifsefegnlna
    hgsgdvkyhlgatgtyiqmfgdndievsltanpshleavdpvleglvrakqdlldtgeeg
    sdnrfsvvplmlhgdaafagqgvvaetlnlallrgyrtggtihivvnnqigfttaptdsr
    sseyctdvakmigapifhvngddpeacawvarlavdfrqafkkdvvidmlcyrrrghneg
    ddpsmtqpymydvidtkrgsrkaytealigrgdismkeaedalrdyqgqlervfnevrel
    ekheiepsesveadqqipsklatavdkamlqrigdahlalpegftvhprvrpvlekrrem
    ayegridwafaellalgsliaegklvrlsgqdtqrgtftqrhavivdrktgeeftplqll
    atnpdgtptggkflvynsalsefaavgfeygysvgnpdamvlweaqfgdfvngaqsiide
    fissgeakwgqlsdvvlllphghegqgpdhtsgrierflqlwaegsmtiampstpanyfh
    llrrhgkdgiqrplivftpksmlrnkaavsdirdfteskfrsvleepmytdgegdrnkvt
    rllltsgkiyyelaarkakenredvaivrieqlaplprrrlaetldrypnvkekfwvqee
    panqgawpsfgltlpeilpdhftglkrisrramsapssgsskvhaveqqeildtafg
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >2yidC (C:)
    gdsiedknarvieliaayrnrghlmadidplrldntrfrshpdldvnshgltlwdldref
    kvdgfagvqrkklrdilsvlrdaycrhvgveythilepeqqrwiqervetkhdkptvaeq
    kyilsklnaaeafetflqtkyvgqkrfslegaetvipmmdavidqcaehgldevviamph
    rgrlnvlanivgkpysqifsefegnlnpsqahgsgdvkyhlgatgtyiqmfgdndievsl
    tanpshleavdpvleglvrakqdlldtgeegsdnrfsvvplmlhgdaafagqgvvaetln
    lallrgyrtggtihivvnnqigfttaptdsrsseyctdvakmigapifhvngddpeacaw
    varlavdfrqafkkdvvidmlcyrrrghnegddpsmtqpymydvidtkrgsrkayteali
    grgdismkeaedalrdyqgqlervfnevrelekheiepsesveadqqipsklatavdkam
    lqrigdahlalpegftvhprvrpvlekrremayegridwafaellalgsliaegklvrls
    gqdtqrgtftqrhavivdrktgeeftplqllatnpdgtptggkflvynsalsefaavgfe
    ygysvgnpdamvlweaqfgdfvngaqsiidefissgeakwgqlsdvvlllphghegqgpd
    htsgrierflqlwaegsmtiampstpanyfhllrrhgkdgiqrplivftpksmlrnkaav
    sdirdfteskfrsvleepmytdgegdrnkvtrllltsgkiyyelaarkakenredvaivr
    ieqlaplprrrlaetldrypnvkekfwvqeepanqgawpsfgltlpeilpdhftglkris
    rramsapssgsskvhaveqqeildtafg
    

    Sequence, based on observed residues (ATOM records):
    >2yidC (C:)
    edknarvieliaayrnrghlmadidplrldntrfrgltlwdldrefkvrkklrdilsvlr
    daycrhvgveythilepeqqrwiqervetkhdkptvaeqkyilsklnaaeafetflqtky
    vgqkrfslegaetvipmmdavidqcaehgldevviamphrgrlnvlanivgkpysqifse
    fegnlnpsqahgsgdvkyhlgatgtyiqmfgdndievsltanpshleavdpvleglvrak
    qdlldtgeegsrfsvvplmlhgdaafagqgvvaetlnlallrgyrtggtihivvnnqigf
    ttaptdsrsseyctdvakmigapifhvngddpeacawvarlavdfrqafkkdvvidmlcy
    rrrghnegddpsmtqpymydvidtkrgsrkaytealigrgdismkeaedalrdyqgqler
    vfnevrelekheiepsesveadqqiklatavdkamlqrigdahlalpegftvhprvrpvl
    ekrremayegridwafaellalgsliaegklvrlsgqdtqrgtftqrhavivdrktgeef
    tplqllatnpdgtptggkflvynsalsefaavgfeygysvgnpdamvlweaqfgdfvnga
    qsiidefissgeakwgqlsdvvlllphghegqgpdhtsgrierflqlwaegsmtiampst
    panyfhllrrhgkdgiqrplivftpksmlrnkaavsdirdfteskfrsvleepmytdgeg
    drnkvtrllltsgkiyyelaarkakenredvaivrieqlaplprrrlaetldrypnvkek
    fwvqeepanqgawpsfgltlpeilpdhftglkrisrramsapssgsskvhaveqqeildt
    afg
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >2yidD (D:)
    gdsiedknarvieliaayrnrghlmadidplrldntrfrshpdldvnshgltlwdldref
    kvdgfagvqrkklrdilsvlrdaycrhvgveythilepeqqrwiqervetkhdkptvaeq
    kyilsklnaaeafetflqtkyvgqkrfslegaetvipmmdavidqcaehgldevviamph
    rgrlnvlanivgkpysqifsefegnlnpsqahgsgdvkyhlgatgtyiqmfgdndievsl
    tanpshleavdpvleglvrakqdlldtgeegsdnrfsvvplmlhgdaafagqgvvaetln
    lallrgyrtggtihivvnnqigfttaptdsrsseyctdvakmigapifhvngddpeacaw
    varlavdfrqafkkdvvidmlcyrrrghnegddpsmtqpymydvidtkrgsrkayteali
    grgdismkeaedalrdyqgqlervfnevrelekheiepsesveadqqipsklatavdkam
    lqrigdahlalpegftvhprvrpvlekrremayegridwafaellalgsliaegklvrls
    gqdtqrgtftqrhavivdrktgeeftplqllatnpdgtptggkflvynsalsefaavgfe
    ygysvgnpdamvlweaqfgdfvngaqsiidefissgeakwgqlsdvvlllphghegqgpd
    htsgrierflqlwaegsmtiampstpanyfhllrrhgkdgiqrplivftpksmlrnkaav
    sdirdfteskfrsvleepmytdgegdrnkvtrllltsgkiyyelaarkakenredvaivr
    ieqlaplprrrlaetldrypnvkekfwvqeepanqgawpsfgltlpeilpdhftglkris
    rramsapssgsskvhaveqqeildtafg
    

    Sequence, based on observed residues (ATOM records):
    >2yidD (D:)
    dsiedknarvieliaayrnrghlmadidplrldntrfrltlwdldrefkvdggvqrkklr
    dilsvlrdaycrhvgveythilepeqqrwiqervetkhdkptvaeqkyilsklnaaeafe
    tflqtkyvgqkrfslegaetvipmmdavidqcaehgldevviamphrgrlnvlanivgkp
    ysqifsefegnlnpsqahgsgdvkyhlgatgtyiqmfgdndievsltanpshleavdpvl
    eglvrakqdlldtgeegsdnrfsvvplmlhgdaafagqgvvaetlnlallrgyrtggtih
    ivvnnqigfttaptdsrsseyctdvakmigapifhvngddpeacawvarlavdfrqafkk
    dvvidmlcyrrrghnegddpsmtqpymydvidtkrgsrkaytealigrgdismkeaedal
    rdyqgqlervfnevrelekheiepsesveadqqiplatavdkamlqrigdahlalpegft
    vhprvrpvlekrremayegridwafaellalgsliaegklvrlsgqdtqrgtftqrhavi
    vdrktgeeftplqllatnpdgtptggkflvynsalsefaavgfeygysvgnpdamvlwea
    qfgdfvngaqsiidefissgeakwgqlsdvvlllphghegqgpdhtsgrierflqlwaeg
    smtiampstpanyfhllrrhgkdgiqrplivftpksmlrnkaavsdirdfteskfrsvle
    epmytdgegdrnkvtrllltsgkiyyelaarkakenredvaivrieqlaplprrrlaetl
    drypnvkekfwvqeepanqgawpsfgltlpeilpdhftglkrisrramsapssgsskvha
    veqqeildtafg