PDB entry 5ws5

View 5ws5 on RCSB PDB site
Description: Native XFEL structure of photosystem II (preflash dark dataset)
Class: photosynthesis
Keywords: photosystem II, photosynthesis, PSII, membrane protein
Deposited on 2016-12-05, released 2017-03-15
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-07-29, with a file datestamp of 2020-07-02.
Experiment type: XRAY
Resolution: 2.35 Å
R-factor: N/A
AEROSPACI score: 0.32 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Photosystem II D1 protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • PDB 5WS5 (Start-343)
  • Chain 'B':
    Compound: Photosystem II CP47 reaction center protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Photosystem II CP43 protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • PDB 5WS5 (Start-454)
  • Chain 'D':
    Compound: Photosystem II D2 protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5d_
  • Chain 'E':
    Compound: Cytochrome b559 subunit alpha
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: Cytochrome b559 subunit beta
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5f_
  • Chain 'H':
    Compound: Photosystem II reaction center protein H
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5h_
  • Chain 'I':
    Compound: Photosystem II reaction center protein I
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5i_
  • Chain 'J':
    Compound: Photosystem II reaction center protein J
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'K':
    Compound: Photosystem II protein K
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • PDB 5WS5 (0-36)
  • Chain 'L':
    Compound: Photosystem II reaction center protein L
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5l_
  • Chain 'M':
    Compound: Photosystem II protein M
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • PDB 5WS5 (0-End)
    Domains in SCOPe 2.08: d5ws5m1, d5ws5m2
  • Chain 'O':
    Compound: Photosystem II manganese-stabilizing polypeptide
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'R':
    Compound: Photosystem II protein Y
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'T':
    Compound: Photosystem II reaction center protein T
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5t_
  • Chain 'U':
    Compound: Photosystem II 12 kDa extrinsic protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5u_
  • Chain 'V':
    Compound: cytochrome c-550
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'X':
    Compound: Photosystem II reaction center protein X
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Y':
    Compound: Photosystem II reaction center protein ycf12
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Z':
    Compound: Photosystem II reaction center protein Z
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'a':
    Compound: Photosystem II D1 protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • PDB 5WS5 (Start-343)
    Domains in SCOPe 2.08: d5ws5a_
  • Chain 'b':
    Compound: Photosystem II CP47 reaction center protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5b_
  • Chain 'c':
    Compound: Photosystem II CP43 protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • PDB 5WS5 (0-454)
    Domains in SCOPe 2.08: d5ws5c_
  • Chain 'd':
    Compound: Photosystem II D2 protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'e':
    Compound: Cytochrome b559 subunit alpha
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5e_
  • Chain 'f':
    Compound: Cytochrome b559 subunit beta
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'h':
    Compound: Photosystem II reaction center protein H
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'i':
    Compound: Photosystem II reaction center protein I
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'j':
    Compound: Photosystem II reaction center protein J
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5j_
  • Chain 'k':
    Compound: Photosystem II protein K
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • PDB 5WS5 (0-36)
    Domains in SCOPe 2.08: d5ws5k_
  • Chain 'l':
    Compound: Photosystem II reaction center protein L
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'm':
    Compound: Photosystem II protein M
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • PDB 5WS5 (0-End)
  • Chain 'o':
    Compound: Photosystem II manganese-stabilizing polypeptide
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5o_
  • Chain 't':
    Compound: Photosystem II reaction center protein T
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'u':
    Compound: Photosystem II 12 kDa extrinsic protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'v':
    Compound: cytochrome c-550
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5v_
  • Chain 'x':
    Compound: Photosystem II reaction center protein X
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5x_
  • Chain 'y':
    Compound: Photosystem II reaction center protein ycf12
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
  • Chain 'z':
    Compound: Photosystem II reaction center protein Z
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ws5z_
  • Heterogens: FE2, CL, CLA, PHO, BCR, SQD, GOL, OEX, PL9, UNL, BCT, LMT, LMG, HTG, DGD, CA, LHG, HEM, MG, HEC, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ws5D (D:)
ergwfdilddwlkrdrfvfvgwsgillfpcaylalggwltgttfvtswythglassyleg
cnfltvavstpansmghsllllwgpeaqgdftrwcqlgglwtfialhgafgligfmlrqf
eiarlvgvrpynaiafsapiavfvsvfliyplgqsswffapsfgvaaifrfllffqgfhn
wtlnpfhmmgvagvlggallcaihgatventlfqdgegastfrafnptqaeetysmvtan
rfwsqifgiafsnkrwlhffmlfvpvtglwmsaigvvglalnlrsydfisqeiraaedpe
fetfytknlllnegirawmapqdqphenfvfpeevlprgnal

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >5ws5F (F:)
tsntpnqepvsypiftvrwvavhtlavptifflgaiaamqfiqr

    Sequence, based on observed residues (ATOM records): (download) 
    >5ws5F (F:)
sypiftvrwvavhtlavptifflgaiaamqfiqr

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >5ws5H (H:)
arrtwlgdilrplnseygkvapgwgttplmavfmglflvflliileiynstlildgvnvs
wkalg

    Sequence, based on observed residues (ATOM records): (download) 
    >5ws5H (H:)
arrtwlgdilrplnseygkvapgwgttplmavfmglflvflliileiynstlildgvnvs
wkal

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ws5I (I:)
metlkitvyivvtffvllfvfgflsgdparnpkrkdle

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    No sequence available.

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >5ws5L (L:)
mepnpnrqpvelnrtslylglllilvlallfssyffn

    Sequence, based on observed residues (ATOM records): (download) 
    >5ws5L (L:)
epnpnrqpvelnrtslylglllilvlallfssyffn

  • Chain 'M':
    Sequence, based on SEQRES records: (download) 
    >5ws5M (M:)
mevnqlgliatalfvlvpsvfliilyvqtesqqkss

    Sequence, based on observed residues (ATOM records): (download) 
    >5ws5M (M:)
mevnqlgliatalfvlvpsvfliilyvqtesqq

  • Chain 'O':
    No sequence available.

  • Chain 'R':
    No sequence available.

  • Chain 'T':
    Sequence, based on SEQRES records: (download) 
    >5ws5T (T:)
metityvfifaciialfffaiffreppritkk

    Sequence, based on observed residues (ATOM records): (download) 
    >5ws5T (T:)
metityvfifaciialfffaiffrepprit

  • Chain 'U':
    Sequence, based on SEQRES records: (download) 
    >5ws5U (U:)
atasteeelvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesved
vlnipglterqkqilrenlehftvtevetalveggdrynnglyk

    Sequence, based on observed residues (ATOM records): (download) 
    >5ws5U (U:)
lvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesvedvlnipglt
erqkqilrenlehftvtevetalveggdrynnglyk

  • Chain 'V':
    No sequence available.

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    No sequence available.

  • Chain 'Z':
    No sequence available.

  • Chain 'a':
    Sequence, based on SEQRES records: (download) 
    >5ws5a (a:)
mtttlqrresanlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdi
dgirepvsgsllygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfl
lgascymgrqwelsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtf
nfmivfqaehnilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfg
qeeetynivaahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngf
nfnhsvidakgnvintwadiinranlgmevmhernahnfpldla

    Sequence, based on observed residues (ATOM records): (download) 
    >5ws5a (a:)
anlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdidgirepvsgs
llygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfllgascymgrq
welsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtfnfmivfqaeh
nilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfgqeeetyniva
ahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngfnfnhsvidak
gnvintwadiinranlgmevmhernahnfpldla

  • Chain 'b':
    Sequence, based on SEQRES records: (download) 
    >5ws5b (b:)
glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
idpelspeqvewgfyqkvgdvttrk

    Sequence, based on observed residues (ATOM records): (download) 
    >5ws5b (b:)
glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
idpelspeqvewgfyqkvgdvttr

  • Chain 'c':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ws5c (c:)
nsifatnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfelahfipe
kpmyeqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyhairgpe
tleeyssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapgggdvrv
itnptldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhilttpfg
warrafiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqaqamtfl
irdqklganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgpngldln
kikndiqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfvlafffl
vghlwhagraraaaagfekgidresepvlsmpsld

  • Chain 'd':
    No sequence available.

  • Chain 'e':
    Sequence, based on SEQRES records: (download) 
    >5ws5e (e:)
magttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeq
rsiplvtdrfeakqqvetfleqlk

    Sequence, based on observed residues (ATOM records): (download) 
    >5ws5e (e:)
gerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeqrsipl
vtdrfeakqqvetfleqlk

  • Chain 'f':
    No sequence available.

  • Chain 'h':
    No sequence available.

  • Chain 'i':
    No sequence available.

  • Chain 'j':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ws5j (j:)
mseggriplwivatvagmgvivivglffygayaglgssl

  • Chain 'k':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ws5k (k:)
klpeayaifdplvdvlpvipvlflalafvwqaavgfr

  • Chain 'l':
    No sequence available.

  • Chain 'm':
    No sequence available.

  • Chain 'o':
    Sequence, based on SEQRES records: (download) 
    >5ws5o (o:)
qtltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqe
aefvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftv
knlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeel
aranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyas
iepa

    Sequence, based on observed residues (ATOM records): (download) 
    >5ws5o (o:)
tltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrqea
efvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllftvk
nlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeeela
ranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfyasi
epa

  • Chain 't':
    No sequence available.

  • Chain 'u':
    No sequence available.

  • Chain 'v':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ws5v (v:)
aeltpevltvplnsegktitltekqylegkrlfqyacaschvggitktnpsldlrtetla
latpprdnieglvdymknpttydgeqeiaevhpslrsadifpkmrnltekdlvaiaghil
vepkilgdkwgggkvyy

  • Chain 'x':
    Sequence, based on SEQRES records: (download) 
    >5ws5x (x:)
titpslkgffigllsgavvlgltfavliaisqidkvqrsl

    Sequence, based on observed residues (ATOM records): (download) 
    >5ws5x (x:)
titpslkgffigllsgavvlgltfavliaisqidkvqr

  • Chain 'y':
    No sequence available.

  • Chain 'z':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ws5z (z:)
mtilfqlalaalvilsfvmvigvpvayaspqdwdrskqliflgsglwialvlvvgvlnff
vv