PDB entry 5oya

View 5oya on RCSB PDB site
Description: Unusual posttranslational modifications revealed in crystal structures of diatom Rubisco.
Class: lyase
Keywords: photosynthesis, carbon dioxide fixation, photorespiration, lyase
Deposited on 2017-09-08, released 2018-06-27
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-06-27, with a file datestamp of 2018-06-22.
Experiment type: XRAY
Resolution: 1.8 Å
R-factor: N/A
AEROSPACI score: 0.37 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Rubisco large subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA
    Domains in SCOPe 2.07: d5oyaa1, d5oyaa2
  • Chain 'B':
    Compound: Rubisco large subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA
    Domains in SCOPe 2.07: d5oyab1, d5oyab2
  • Chain 'C':
    Compound: Rubisco large subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA
    Domains in SCOPe 2.07: d5oyac1, d5oyac2
  • Chain 'D':
    Compound: Rubisco large subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA
    Domains in SCOPe 2.07: d5oyad1, d5oyad2
  • Chain 'E':
    Compound: Rubisco large subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA
    Domains in SCOPe 2.07: d5oyae1, d5oyae2
  • Chain 'F':
    Compound: Rubisco large subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA
    Domains in SCOPe 2.07: d5oyaf1, d5oyaf2
  • Chain 'G':
    Compound: Rubisco large subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA
    Domains in SCOPe 2.07: d5oyag1, d5oyag2
  • Chain 'H':
    Compound: Rubisco large subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA
    Domains in SCOPe 2.07: d5oyah1, d5oyah2
  • Chain 'I':
    Compound: Rubisco small subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA (0-138)
    Domains in SCOPe 2.07: d5oyai_
  • Chain 'J':
    Compound: Rubisco small subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA (0-138)
    Domains in SCOPe 2.07: d5oyaj_
  • Chain 'K':
    Compound: Rubisco small subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA (0-138)
    Domains in SCOPe 2.07: d5oyak_
  • Chain 'L':
    Compound: Rubisco small subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA (0-138)
    Domains in SCOPe 2.07: d5oyal_
  • Chain 'M':
    Compound: Rubisco small subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA (0-138)
    Domains in SCOPe 2.07: d5oyam_
  • Chain 'N':
    Compound: Rubisco small subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA (0-138)
    Domains in SCOPe 2.07: d5oyan_
  • Chain 'O':
    Compound: Rubisco small subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA (0-138)
    Domains in SCOPe 2.07: d5oyao_
  • Chain 'P':
    Compound: Rubisco small subunit
    Species: Chaetoceros socialis [TaxId:163503]
    Database cross-references and differences (RAF-indexed):
    • PDB 5OYA (0-138)
    Domains in SCOPe 2.07: d5oyap_
  • Heterogens: MG, CAP, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5oyaA (A:)
    msqsvsertriksdryesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaa
    vagesstatwtvvwtdlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanl
    tasiignvfgfkaisalrledmriphsylxtfqgpatgiivererlnkygtplxgatvkp
    klglsgknygrvvyeglkggldflkddeninsqpfmrwrerflncleginrasaatgevk
    gsylnvtaatmeevykraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhrag
    nstyarqknhginfrvickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevn
    lpfgiffemdwaslrrcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqaga
    tanrvaleamvlarnegadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdta
    dfsetatanr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5oyaA (A:)
    yesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaavagesstatwtvvwt
    dlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanltasiignvfgfkais
    alrledmriphsylxtfqgpatgiivererlnkygtplxgatvkpklglsgknygrvvye
    glkggldflkddeninsqpfmrwrerflncleginrasaatgevkgsylnvtaatmeevy
    kraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhragnstyarqknhginfr
    vickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevnlpfgiffemdwaslr
    rcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqagatanrvaleamvlarn
    egadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdtadfs
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5oyaB (B:)
    msqsvsertriksdryesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaa
    vagesstatwtvvwtdlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanl
    tasiignvfgfkaisalrledmriphsylxtfqgpatgiivererlnkygtplxgatvkp
    klglsgknygrvvyeglkggldflkddeninsqpfmrwrerflncleginrasaatgevk
    gsylnvtaatmeevykraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhrag
    nstyarqknhginfrvickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevn
    lpfgiffemdwaslrrcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqaga
    tanrvaleamvlarnegadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdta
    dfsetatanr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5oyaB (B:)
    ryesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaavagesstatwtvvw
    tdlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanltasiignvfgfkai
    salrledmriphsylxtfqgpatgiivererlnkygtplxgatvkpklglsgknygrvvy
    eglkggldflkddeninsqpfmrwrerflncleginrasaatgevkgsylnvtaatmeev
    ykraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhragnstyarqknhginf
    rvickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevnlpfgiffemdwasl
    rrcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqagatanrvaleamvlar
    negadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdtadfs
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5oyaC (C:)
    msqsvsertriksdryesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaa
    vagesstatwtvvwtdlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanl
    tasiignvfgfkaisalrledmriphsylxtfqgpatgiivererlnkygtplxgatvkp
    klglsgknygrvvyeglkggldflkddeninsqpfmrwrerflncleginrasaatgevk
    gsylnvtaatmeevykraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhrag
    nstyarqknhginfrvickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevn
    lpfgiffemdwaslrrcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqaga
    tanrvaleamvlarnegadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdta
    dfsetatanr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5oyaC (C:)
    yesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaavagesstatwtvvwt
    dlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanltasiignvfgfkais
    alrledmriphsylxtfqgpatgiivererlnkygtplxgatvkpklglsgknygrvvye
    glkggldflkddeninsqpfmrwrerflncleginrasaatgevkgsylnvtaatmeevy
    kraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhragnstyarqknhginfr
    vickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevnlpfgiffemdwaslr
    rcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqagatanrvaleamvlarn
    egadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdtadfs
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5oyaD (D:)
    msqsvsertriksdryesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaa
    vagesstatwtvvwtdlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanl
    tasiignvfgfkaisalrledmriphsylxtfqgpatgiivererlnkygtplxgatvkp
    klglsgknygrvvyeglkggldflkddeninsqpfmrwrerflncleginrasaatgevk
    gsylnvtaatmeevykraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhrag
    nstyarqknhginfrvickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevn
    lpfgiffemdwaslrrcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqaga
    tanrvaleamvlarnegadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdta
    dfsetatanr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5oyaD (D:)
    yesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaavagesstatwtvvwt
    dlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanltasiignvfgfkais
    alrledmriphsylxtfqgpatgiivererlnkygtplxgatvkpklglsgknygrvvye
    glkggldflkddeninsqpfmrwrerflncleginrasaatgevkgsylnvtaatmeevy
    kraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhragnstyarqknhginfr
    vickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevnlpfgiffemdwaslr
    rcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqagatanrvaleamvlarn
    egadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdtadfs
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5oyaE (E:)
    msqsvsertriksdryesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaa
    vagesstatwtvvwtdlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanl
    tasiignvfgfkaisalrledmriphsylxtfqgpatgiivererlnkygtplxgatvkp
    klglsgknygrvvyeglkggldflkddeninsqpfmrwrerflncleginrasaatgevk
    gsylnvtaatmeevykraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhrag
    nstyarqknhginfrvickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevn
    lpfgiffemdwaslrrcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqaga
    tanrvaleamvlarnegadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdta
    dfsetatanr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5oyaE (E:)
    ryesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaavagesstatwtvvw
    tdlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanltasiignvfgfkai
    salrledmriphsylxtfqgpatgiivererlnkygtplxgatvkpklglsgknygrvvy
    eglkggldflkddeninsqpfmrwrerflncleginrasaatgevkgsylnvtaatmeev
    ykraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhragnstyarqknhginf
    rvickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevnlpfgiffemdwasl
    rrcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqagatanrvaleamvlar
    negadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdtadfs
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5oyaF (F:)
    msqsvsertriksdryesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaa
    vagesstatwtvvwtdlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanl
    tasiignvfgfkaisalrledmriphsylxtfqgpatgiivererlnkygtplxgatvkp
    klglsgknygrvvyeglkggldflkddeninsqpfmrwrerflncleginrasaatgevk
    gsylnvtaatmeevykraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhrag
    nstyarqknhginfrvickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevn
    lpfgiffemdwaslrrcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqaga
    tanrvaleamvlarnegadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdta
    dfsetatanr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5oyaF (F:)
    ryesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaavagesstatwtvvw
    tdlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanltasiignvfgfkai
    salrledmriphsylxtfqgpatgiivererlnkygtplxgatvkpklglsgknygrvvy
    eglkggldflkddeninsqpfmrwrerflncleginrasaatgevkgsylnvtaatmeev
    ykraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhragnstyarqknhginf
    rvickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevnlpfgiffemdwasl
    rrcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqagatanrvaleamvlar
    negadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdtadfs
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5oyaG (G:)
    msqsvsertriksdryesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaa
    vagesstatwtvvwtdlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanl
    tasiignvfgfkaisalrledmriphsylxtfqgpatgiivererlnkygtplxgatvkp
    klglsgknygrvvyeglkggldflkddeninsqpfmrwrerflncleginrasaatgevk
    gsylnvtaatmeevykraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhrag
    nstyarqknhginfrvickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevn
    lpfgiffemdwaslrrcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqaga
    tanrvaleamvlarnegadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdta
    dfsetatanr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5oyaG (G:)
    ryesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaavagesstatwtvvw
    tdlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanltasiignvfgfkai
    salrledmriphsylxtfqgpatgiivererlnkygtplxgatvkpklglsgknygrvvy
    eglkggldflkddeninsqpfmrwrerflncleginrasaatgevkgsylnvtaatmeev
    ykraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhragnstyarqknhginf
    rvickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevnlpfgiffemdwasl
    rrcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqagatanrvaleamvlar
    negadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdtadfs
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >5oyaH (H:)
    msqsvsertriksdryesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaa
    vagesstatwtvvwtdlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanl
    tasiignvfgfkaisalrledmriphsylxtfqgpatgiivererlnkygtplxgatvkp
    klglsgknygrvvyeglkggldflkddeninsqpfmrwrerflncleginrasaatgevk
    gsylnvtaatmeevykraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhrag
    nstyarqknhginfrvickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevn
    lpfgiffemdwaslrrcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqaga
    tanrvaleamvlarnegadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdta
    dfsetatanr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5oyaH (H:)
    yesgvipyakmgywdaaytvkdtdvlalfritpqpgvdpveaaaavagesstatwtvvwt
    dlltaceryrakayrvdpvpnstdvyfafiayecdlfeeaslanltasiignvfgfkais
    alrledmriphsylxtfqgpatgiivererlnkygtplxgatvkpklglsgknygrvvye
    glkggldflkddeninsqpfmrwrerflncleginrasaatgevkgsylnvtaatmeevy
    kraeyakaigsivvmidlvmgytaiqsiaywarendmllhlhragnstyarqknhginfr
    vickwmrmsgvdhihagtvvgklegdplmikgfydilrltelevnlpfgiffemdwaslr
    rcmpvasggihcgqmhqlihylgddvvlqfgggtighpdgiqagatanrvaleamvlarn
    egadyfnnqvgpqilrdaaktcgplqtaldlwkdisfnytstdtadfs
    

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5oyaI (I:)
    mrltqgcfsflpdltdaqiekqvayamsrgwamnvewtddphprnnywelwglplfdikd
    patvmfelnearkscaagyirmnafdasygtescvmsfltnrpanepgfyldrtdgigrq
    iiysiksysvqanpegsry
    

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5oyaJ (J:)
    mrltqgcfsflpdltdaqiekqvayamsrgwamnvewtddphprnnywelwglplfdikd
    patvmfelnearkscaagyirmnafdasygtescvmsfltnrpanepgfyldrtdgigrq
    iiysiksysvqanpegsry
    

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5oyaK (K:)
    mrltqgcfsflpdltdaqiekqvayamsrgwamnvewtddphprnnywelwglplfdikd
    patvmfelnearkscaagyirmnafdasygtescvmsfltnrpanepgfyldrtdgigrq
    iiysiksysvqanpegsry
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5oyaL (L:)
    mrltqgcfsflpdltdaqiekqvayamsrgwamnvewtddphprnnywelwglplfdikd
    patvmfelnearkscaagyirmnafdasygtescvmsfltnrpanepgfyldrtdgigrq
    iiysiksysvqanpegsry
    

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5oyaM (M:)
    mrltqgcfsflpdltdaqiekqvayamsrgwamnvewtddphprnnywelwglplfdikd
    patvmfelnearkscaagyirmnafdasygtescvmsfltnrpanepgfyldrtdgigrq
    iiysiksysvqanpegsry
    

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5oyaN (N:)
    mrltqgcfsflpdltdaqiekqvayamsrgwamnvewtddphprnnywelwglplfdikd
    patvmfelnearkscaagyirmnafdasygtescvmsfltnrpanepgfyldrtdgigrq
    iiysiksysvqanpegsry
    

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5oyaO (O:)
    mrltqgcfsflpdltdaqiekqvayamsrgwamnvewtddphprnnywelwglplfdikd
    patvmfelnearkscaagyirmnafdasygtescvmsfltnrpanepgfyldrtdgigrq
    iiysiksysvqanpegsry
    

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5oyaP (P:)
    mrltqgcfsflpdltdaqiekqvayamsrgwamnvewtddphprnnywelwglplfdikd
    patvmfelnearkscaagyirmnafdasygtescvmsfltnrpanepgfyldrtdgigrq
    iiysiksysvqanpegsry