PDB entry 5kaf

View 5kaf on RCSB PDB site
Description: RT XFEL structure of Photosystem II in the dark state at 3.0 A resolution
Class: electron transport
Keywords: photosystems, transmembrane, room temperature, electron transport
Deposited on 2016-06-01, released 2016-11-23
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-03-10, with a file datestamp of 2021-03-05.
Experiment type: XRAY
Resolution: 3 Å
R-factor: N/A
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Photosystem II protein D1 1
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafa_
  • Chain 'B':
    Compound: Photosystem II CP47 reaction center protein
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafb_
  • Chain 'C':
    Compound: Photosystem II CP43 reaction center protein
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafc_
  • Chain 'D':
    Compound: Photosystem II D2 protein
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafd_
  • Chain 'E':
    Compound: Cytochrome b559 subunit alpha
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafe_
  • Chain 'F':
    Compound: Cytochrome b559 subunit beta
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: Photosystem II reaction center protein H
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafh_
  • Chain 'I':
    Compound: Photosystem II reaction center protein I
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8DJZ6 (1-End)
      • expression tag (0)
    Domains in SCOPe 2.08: d5kafi1, d5kafi2
  • Chain 'J':
    Compound: Photosystem II reaction center protein J
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafj_
  • Chain 'K':
    Compound: Photosystem II reaction center protein K
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: Photosystem II reaction center protein L
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: Photosystem II reaction center protein M
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8DHA7 (1-End)
      • expression tag (0)
    Domains in SCOPe 2.08: d5kafm1, d5kafm2
  • Chain 'O':
    Compound: Photosystem II manganese-stabilizing polypeptide
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'R':
    Compound: Photosystem II protein Y
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'T':
    Compound: Photosystem II reaction center protein T
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8DIQ0 (1-End)
      • expression tag (0)
    Domains in SCOPe 2.08: d5kaft1, d5kaft2
  • Chain 'U':
    Compound: Photosystem II 12 kDa extrinsic protein
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafu_
  • Chain 'V':
    Compound: cytochrome c-550
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'X':
    Compound: Photosystem II reaction center X protein
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafx_
  • Chain 'Y':
    Compound: Photosystem II reaction center protein ycf12
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Z':
    Compound: Photosystem II reaction center protein Z
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafz_
  • Chain 'a':
    Compound: Photosystem II protein D1 1
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'b':
    Compound: Photosystem II CP47 reaction center protein
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'c':
    Compound: Photosystem II CP43 reaction center protein
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'd':
    Compound: Photosystem II D2 protein
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'e':
    Compound: Cytochrome b559 subunit alpha
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'f':
    Compound: Cytochrome b559 subunit beta
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kaff_
  • Chain 'h':
    Compound: Photosystem II reaction center protein H
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'i':
    Compound: Photosystem II reaction center protein I
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8DJZ6 (1-End)
      • expression tag (0)
  • Chain 'j':
    Compound: Photosystem II reaction center protein J
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'k':
    Compound: Photosystem II reaction center protein K
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafk_
  • Chain 'l':
    Compound: Photosystem II reaction center protein L
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafl_
  • Chain 'm':
    Compound: Photosystem II reaction center protein M
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8DHA7 (1-End)
      • expression tag (0)
  • Chain 'o':
    Compound: Photosystem II manganese-stabilizing polypeptide
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafo_
  • Chain 'r':
    Compound: Photosystem II protein Y
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 't':
    Compound: Photosystem II reaction center protein T
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8DIQ0 (1-End)
      • expression tag (0)
  • Chain 'u':
    Compound: Photosystem II 12 kDa extrinsic protein
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'v':
    Compound: cytochrome c-550
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5kafv_
  • Chain 'x':
    Compound: Photosystem II reaction center X protein
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'y':
    Compound: Photosystem II reaction center protein ycf12
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Chain 'z':
    Compound: Photosystem II reaction center protein Z
    Species: Thermosynechococcus elongatus (strain BP-1) [TaxId:197221]
    Database cross-references and differences (RAF-indexed):
  • Heterogens: OEX, FE2, SQD, CL, CLA, PHO, BCR, PL9, LMG, UNL, LHG, BCT, DGD, HEM, HEC, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5kafA (A:)
    mtttlqrresanlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdi
    dgirepvsgsllygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfl
    lgascymgrqwelsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtf
    nfmivfqaehnilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfg
    qeeetynivaahgyfgrlifqyasfnnsrslhfflaawpvvgvwftalgistmafnlngf
    nfnhsvidakgnvintwadiinranlgmevmhernahnfpldla
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafA (A:)
    anlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdidgirepvsgs
    llygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfllgascymgrq
    welsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtfnfmivfqaeh
    nilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfgqeeetyniva
    ahgyfgrlifqyasfnnsrslhfflaawpvvgvwftalgistmafnlngfnfnhsvidak
    gnvintwadiinranlgmevmhernahnfpldla
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5kafB (B:)
    mglpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgm
    fvlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdl
    elfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqp
    vapewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlss
    siaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatlee
    awsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmp
    affesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksy
    arkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfs
    gidpelspeqvewgfyqkvgdvttrrkeav
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafB (B:)
    glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
    vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
    lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
    apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
    iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
    wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
    ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
    rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
    idpelspeqvewgfyqkvgdvttr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5kafC (C:)
    mvtlssnsifatnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfel
    ahfipekpmyeqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyh
    airgpetleeyssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapg
    ggdvrvitnptldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhi
    lttpfgwarrafiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqa
    qamtflirdqklganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgp
    ngldlnkikndiqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfv
    laffflvghlwhagraraaaagfekgidresepvlsmpsld
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafC (C:)
    atnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfelahfipekpmy
    eqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyhairgpetlee
    yssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapgggdvrvitnp
    tldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhilttpfgwarr
    afiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqaqamtflirdq
    klganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgpngldlnkikn
    diqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfvlaffflvghl
    whagraraaaagfekgidresepvlsmpsld
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5kafD (D:)
    mtiaigrapaergwfdilddwlkrdrfvfvgwsgillfpcaylalggwltgttfvtswyt
    hglassylegcnfltvavstpansmghsllllwgpeaqgdftrwcqlgglwtfialhgaf
    gligfmlrqfeiarlvgvrpynaiafsapiavfvsvfliyplgqsswffapsfgvaaifr
    fllffqgfhnwtlnpfhmmgvagvlggallcaihgatventlfqdgegastfrafnptqa
    eetysmvtanrfwsqifgiafsnkrwlhffmlfvpvtglwmsaigvvglalnlrsydfis
    qeiraaedpefetfytknlllnegirawmapqdqphenfvfpeevlprgnal
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafD (D:)
    rgwfdilddwlkrdrfvfvgwsgillfpcaylalggwltgttfvtswythglassylegc
    nfltvavstpansmghsllllwgpeaqgdftrwcqlgglwtfialhgafgligfmlrqfe
    iarlvgvrpynaiafsapiavfvsvfliyplgqsswffapsfgvaaifrfllffqgfhnw
    tlnpfhmmgvagvlggallcaihgatventlfqdgegastfrafnptqaeetysmvtanr
    fwsqifgiafsnkrwlhffmlfvpvtglwmsaigvvglalnlrsydfisqeiraaedpef
    etfytknlllnegirawmapqdqphenfvfpeevlprgnal
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5kafE (E:)
    magttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeq
    rsiplvtdrfeakqqvetfleqlk
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafE (E:)
    ttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeqrsi
    plvtdrfeakqqvetfleqlk
    

  • Chain 'F':
    No sequence available.

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >5kafH (H:)
    marrtwlgdilrplnseygkvapgwgttplmavfmglflvflliileiynstlildgvnv
    swkalg
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafH (H:)
    arrtwlgdilrplnseygkvapgwgttplmavfmglflvflliileiynstlildgvnvs
    wka
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >5kafI (I:)
    metlkitvyivvtffvllfvfgflsgdparnpkrkdle
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafI (I:)
    metlkitvyivvtffvllfvfgflsgdparnpkrkd
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >5kafJ (J:)
    mmseggriplwivatvagmgvivivglffygayaglgssl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafJ (J:)
    ggriplwivatvagmgvivivglffygayaglgssl
    

  • Chain 'K':
    No sequence available.

  • Chain 'L':
    No sequence available.

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >5kafM (M:)
    mevnqlgliatalfvlvpsvfliilyvqtesqqkss
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafM (M:)
    mevnqlgliatalfvlvpsvfliilyvqtesqq
    

  • Chain 'O':
    No sequence available.

  • Chain 'R':
    No sequence available.

  • Chain 'T':
    Sequence, based on SEQRES records: (download)
    >5kafT (T:)
    metityvfifaciialfffaiffreppritkk
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafT (T:)
    metityvfifaciialfffaiffrepprit
    

  • Chain 'U':
    Sequence, based on SEQRES records: (download)
    >5kafU (U:)
    mqrlgrwlalayfvgvsllgwinwsaptlaatasteeelvnvvdeklgtaygekidlnnt
    niaafiqyrglyptlaklivknapyesvedvlnipglterqkqilrenlehftvteveta
    lveggdrynnglyk
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafU (U:)
    elvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesvedvlnipgl
    terqkqilrenlehftvtevetalveggdrynnglyk
    

  • Chain 'V':
    No sequence available.

  • Chain 'X':
    Sequence, based on SEQRES records: (download)
    >5kafX (X:)
    mtitpslkgffigllsgavvlgltfavliaisqidkvqrsl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafX (X:)
    titpslkgffigllsgavvlgltfavliaisqidkvqr
    

  • Chain 'Y':
    No sequence available.

  • Chain 'Z':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5kafZ (Z:)
    mtilfqlalaalvilsfvmvigvpvayaspqdwdrskqliflgsglwialvlvvgvlnff
    vv
    

  • Chain 'a':
    No sequence available.

  • Chain 'b':
    No sequence available.

  • Chain 'c':
    No sequence available.

  • Chain 'd':
    No sequence available.

  • Chain 'e':
    No sequence available.

  • Chain 'f':
    Sequence, based on SEQRES records: (download)
    >5kaff (f:)
    mtsntpnqepvsypiftvrwvavhtlavptifflgaiaamqfiqr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kaff (f:)
    sypiftvrwvavhtlavptifflgaiaamqfiqr
    

  • Chain 'h':
    No sequence available.

  • Chain 'i':
    No sequence available.

  • Chain 'j':
    No sequence available.

  • Chain 'k':
    Sequence, based on SEQRES records: (download)
    >5kafk (k:)
    midalvlvaklpeayaifdplvdvlpvipvlflalafvwqaavgfr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafk (k:)
    klpeayaifdplvdvlpvipvlflalafvwqaavgfr
    

  • Chain 'l':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5kafl (l:)
    mepnpnrqpvelnrtslylglllilvlallfssyffn
    

  • Chain 'm':
    No sequence available.

  • Chain 'o':
    Sequence, based on SEQRES records: (download)
    >5kafo (o:)
    mkyrilmatllavclgifslsapafaakqtltyddivgtglankcptlddtargaypids
    sqtyriarlclqpttflvkeepknkrqeaefvptklvtrettsldqiqgelkvnsdgslt
    fveedgidfqpvtvqmaggeripllftvknlvastqpnvtsittstdfkgefnvpsyrta
    nfldpkgrglasgydsaialpqakeeelaranvkrfsltkgqislnvakvdgrtgeiagt
    feseqlsdddmgahephevkiqgvfyasiepa
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafo (o:)
    qtltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqe
    aefvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftv
    knlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeel
    aranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyas
    iepa
    

  • Chain 'r':
    No sequence available.

  • Chain 't':
    No sequence available.

  • Chain 'u':
    No sequence available.

  • Chain 'v':
    Sequence, based on SEQRES records: (download)
    >5kafv (v:)
    mlkkcvwlavalclclwqftmgtalaaeltpevltvplnsegktitltekqylegkrlfq
    yacaschvggitktnpsldlrtetlalatpprdnieglvdymknpttydgeqeiaevhps
    lrsadifpkmrnltekdlvaiaghilvepkilgdkwgggkvyy
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kafv (v:)
    aeltpevltvplnsegktitltekqylegkrlfqyacaschvggitktnpsldlrtetla
    latpprdnieglvdymknpttydgeqeiaevhpslrsadifpkmrnltekdlvaiaghil
    vepkilgdkwgggkvyy
    

  • Chain 'x':
    No sequence available.

  • Chain 'y':
    No sequence available.

  • Chain 'z':
    No sequence available.