PDB entry 5b5e

View 5b5e on RCSB PDB site
Description: Crystal structure analysis of Photosystem II complex
Class: electron transport, photosynthesis
Keywords: psii, electron transport, photosynthesis, photosystem, membrane complex, transmembrane alpha-helix, oxygen evolving, water splitting, iron binding, calcium binding, manganese binding, chloride binding, formylation, hydroxylation, thylakoid membrane
Deposited on 2016-05-02, released 2017-02-01
The last revision prior to the SCOPe 2.06 freeze date was dated 2017-02-01, with a file datestamp of 2017-01-26.
Experiment type: XRAY
Resolution: 1.87 Å
R-factor: N/A
AEROSPACI score: 0.34 (click here for full SPACI score report)

Chains and heterogens:

• Chain 'A':
  Compound: Photosystem II protein D1
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P51765 (Start-343)
    • see sequence details (278)
• Chain 'B':
  Compound: Photosystem II CP47 reaction center protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR1 (0-504)
• Chain 'C':
  Compound: Photosystem II CP43 reaction center protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR7 (4-454)
• Chain 'D':
  Compound: Photosystem II D2 protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR8 (0-341)
• Chain 'E':
  Compound: Cytochrome b559 subunit alpha
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12238 (Start-82)
• Chain 'F':
  Compound: Cytochrome b559 subunit beta
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12239 (Start-43)
  Domains in SCOPe 2.06: d5b5ef_
• Chain 'H':
  Compound: Photosystem II reaction center protein H
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P19052 (0-End)
  Domains in SCOPe 2.06: d5b5eh_
• Chain 'I':
  Compound: Photosystem II reaction center protein I
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12240 (0-End)
  Domains in SCOPe 2.06: d5b5ei_
• Chain 'J':
  Compound: Photosystem II reaction center protein J
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q7DGD4 (Start-39)
• Chain 'K':
  Compound: Photosystem II reaction center protein K
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P19054 (0-36)
    • see sequence details (23)
    • see sequence details (29)
• Chain 'L':
  Compound: Photosystem II reaction center protein L
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12241 (0-36)
  Domains in SCOPe 2.06: d5b5el_
• Chain 'M':
  Compound: Photosystem II reaction center protein M
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12312 (0-End)
    • see sequence details (7)
• Chain 'O':
  Compound: Photosystem II manganese-stabilizing polypeptide
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR2 (Start-243)
• Chain 'T':
  Compound: Photosystem II reaction center protein T
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12313 (0-End)
• Chain 'U':
  Compound: Photosystem II 12 kDa extrinsic protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P56152 (Start-103)
• Chain 'V':
  Compound: cytochrome c-550
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A387 (0-136)
• Chain 'X':
  Compound: Photosystem II reaction center protein X
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR4 (0-End)
  Domains in SCOPe 2.06: d5b5ex_
• Chain 'Y':
  Compound: Photosystem II reaction center protein ycf12
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR3 (Start-29)
• Chain 'Z':
  Compound: Photosystem II reaction center protein Z
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR5 (0-61)
  Domains in SCOPe 2.06: d5b5ez_
• Chain 'a':
  Compound: Photosystem II protein D1
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P51765 (Start-343)
    • see sequence details (278)
  Domains in SCOPe 2.06: d5b5ea_
• Chain 'b':
  Compound: Photosystem II CP47 reaction center protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR1 (0-End)
• Chain 'c':
  Compound: Photosystem II CP43 reaction center protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR7 (4-454)
    • see sequence details (0-3)
• Chain 'd':
  Compound: Photosystem II D2 protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR8 (0-341)
• Chain 'e':
  Compound: Cytochrome b559 subunit alpha
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12238 (Start-82)
• Chain 'f':
  Compound: Cytochrome b559 subunit beta
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12239 (Start-43)
• Chain 'h':
  Compound: Photosystem II reaction center protein H
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P19052 (0-End)
• Chain 'i':
  Compound: Photosystem II reaction center protein I
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12240 (0-37)
• Chain 'j':
  Compound: Photosystem II reaction center protein J
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q7DGD4 (0-39)
  Domains in SCOPe 2.06: d5b5ej_
• Chain 'k':
  Compound: Photosystem II reaction center protein K
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P19054 (0-36)
    • see sequence details (23)
    • see sequence details (29)
• Chain 'l':
  Compound: Photosystem II reaction center protein L
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12241 (Start-36)
• Chain 'm':
  Compound: Photosystem II reaction center protein M
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12312 (0-End)
    • see sequence details (7)
• Chain 'o':
  Compound: Photosystem II manganese-stabilizing polypeptide
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR2 (Start-243)
• Chain 't':
  Compound: Photosystem II reaction center protein T
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P12313 (0-End)
• Chain 'u':
  Compound: Photosystem II 12 kDa extrinsic protein
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P56152 (Start-103)
• Chain 'v':
  Compound: cytochrome c-550
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A387 (0-136)
  Domains in SCOPe 2.06: d5b5ev_
• Chain 'x':
  Compound: Photosystem II reaction center protein X
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR4 (0-End)
• Chain 'y':
  Compound: Photosystem II reaction center protein ycf12
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR3 (Start-29)
• Chain 'z':
  Compound: Photosystem II reaction center protein Z
  Species: Thermosynechococcus vulcanus [TaxId:32053]
  Database cross-references and differences (RAF-indexed):
  • Uniprot D0VWR5 (0-End)
• Heterogens: OEX, FE2, CL, CLA, PHO, BCR, SQD, PL9, LHG, UNL, LMT, DMS, BCT, CA, LMG, HTG, DGD, HEM, RRX, MG, HOH

PDB Chain Sequences:

• 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)
  

  >5b5eF (F:)
  tsntpnqepvsypiftvrwvavhtlavptifflgaiaamqfiqr
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >5b5eF (F:)
  vsypiftvrwvavhtlavptifflgaiaamqfiqr
  

  
  
• Chain 'H':
  Sequence, based on SEQRES records: (download)
  

  >5b5eH (H:)
  arrtwlgdilrplnseygkvapgwgttplmavfmglflvflliileiynstlildgvnvs
  wkalg
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >5b5eH (H:)
  arrtwlgdilrplnseygkvapgwgttplmavfmglflvflliileiynstlildgvnvs
  wka
  

  
  
• Chain 'I':
  Sequence, based on SEQRES records: (download)
  

  >5b5eI (I:)
  metlkitvyivvtffvllfvfgflsgdparnpkrkdle
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >5b5eI (I:)
  metlkitvyivvtffvllfvfgflsgdparnpkrk
  

  
  
• Chain 'J':
  No sequence available.
  
  
• Chain 'K':
  No sequence available.
  
  
• Chain 'L':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >5b5eL (L:)
  mepnpnrqpvelnrtslylglllilvlallfssyffn
  

  
  
• Chain 'M':
  No sequence available.
  
  
• Chain 'O':
  No sequence available.
  
  
• Chain 'T':
  No sequence available.
  
  
• Chain 'U':
  No sequence available.
  
  
• Chain 'V':
  No sequence available.
  
  
• Chain 'X':
  Sequence, based on SEQRES records: (download)
  

  >5b5eX (X:)
  titpslkgffigllsgavvlgltfavliaisqidkvqrsl
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >5b5eX (X:)
  titpslkgffigllsgavvlgltfavliaisqidkvqr
  

  
  
• Chain 'Y':
  No sequence available.
  
  
• Chain 'Z':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >5b5eZ (Z:)
  mtilfqlalaalvilsfvmvigvpvayaspqdwdrskqliflgsglwialvlvvgvlnff
  vv
  

  
  
• Chain 'a':
  Sequence, based on SEQRES records: (download)
  

  >5b5ea (a:)
  mtttlqrresanlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdi
  dgirepvsgsllygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfl
  lgascymgrqwelsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtf
  nfmivfqaehnilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfg
  qeeetynivaahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngf
  nfnhsvidakgnvintwadiinranlgmevmhernahnfpldla
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >5b5ea (a:)
  anlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdidgirepvsgs
  llygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfllgascymgrq
  welsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtfnfmivfqaeh
  nilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfgqeeetyniva
  ahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngfnfnhsvidak
  gnvintwadiinranlgmevmhernahnfpldla
  

  
  
• Chain 'b':
  No sequence available.
  
  
• Chain 'c':
  No sequence available.
  
  
• Chain 'd':
  No sequence available.
  
  
• Chain 'e':
  No sequence available.
  
  
• 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)
  

  >5b5ej (j:)
  mmseggriplwivatvagmgvivivglffygayaglgssl
  

  
  
• Chain 'k':
  No sequence available.
  
  
• Chain 'l':
  No sequence available.
  
  
• Chain 'm':
  No sequence available.
  
  
• Chain 'o':
  No sequence available.
  
  
• Chain 't':
  No sequence available.
  
  
• Chain 'u':
  No sequence available.
  
  
• Chain 'v':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >5b5ev (v:)
  aeltpevltvplnsegktitltekqylegkrlfqyacaschvggitktnpsldlrtetla
  latpprdnieglvdymknpttydgeqeiaevhpslrsadifpkmrnltekdlvaiaghil
  vepkilgdkwgggkvyy
  

  
  
• Chain 'x':
  No sequence available.
  
  
• Chain 'y':
  No sequence available.
  
  
• Chain 'z':
  No sequence available.