PDB entry 5v2c

View 5v2c on RCSB PDB site
Description: re-refinement of crystal structure of photosystem II complex
Class: electron transport, photosynthesis
Keywords: electron transport, photosynthesis
Deposited on 2017-03-03, released 2017-08-30
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: 1.9 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)
      • conflict (278)
    Domains in SCOPe 2.08: d5v2ca_
  • 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: d5v2cb_
  • Chain 'C':
    Compound: Photosystem II CP43 reaction center protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v2cc_
  • Chain 'D':
    Compound: Photosystem II D2 protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v2cd_
  • Chain 'E':
    Compound: Cytochrome b559 subunit alpha
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v2ce_
  • Chain 'F':
    Compound: Cytochrome b559 subunit beta
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v2cf_
  • 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: d5v2ch_
  • 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: d5v2ci_
  • 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)
      • conflict (1)
    Domains in SCOPe 2.08: d5v2cj_
  • 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)
      • conflict (23)
      • conflict (29)
    Domains in SCOPe 2.08: d5v2ck_
  • 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: d5v2cl_
  • 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)
      • conflict (7)
    Domains in SCOPe 2.08: d5v2cm_
  • Chain 'O':
    Compound: Photosystem II manganese-stabilizing polypeptide
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • Uniprot D0VWR2 (2-244)
      • expression tag (0-1)
    Domains in SCOPe 2.08: d5v2co1, d5v2co2
  • 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: d5v2ct_
  • 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: d5v2cu_
  • Chain 'V':
    Compound: cytochrome c-550
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v2cv_
  • Chain 'X':
    Compound: Photosystem II reaction center protein X
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • Uniprot D0VWR4 (1-End)
      • initiating methionine (0)
    Domains in SCOPe 2.08: d5v2cx_
  • 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: d5v2cz_
  • Chain 'a':
    Compound: Photosystem II protein D1
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P51765 (Start-343)
      • conflict (278)
  • Chain 'b':
    Compound: Photosystem II CP47 reaction center protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • Uniprot D0VWR1 (0-503)
      • expression tag (504-505)
  • Chain 'c':
    Compound: Photosystem II CP43 reaction center protein
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • Uniprot D0VWR7 (7-457)
      • expression tag (0-6)
  • 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):
  • 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):
    • Uniprot Q7DGD4 (Start-39)
      • conflict (1)
  • 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)
      • conflict (23)
      • conflict (29)
  • 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 reaction center protein M
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P12312 (0-End)
      • conflict (7)
  • Chain 'o':
    Compound: Photosystem II manganese-stabilizing polypeptide
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • Uniprot D0VWR2 (2-244)
      • expression tag (0-1)
  • 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):
  • Chain 'x':
    Compound: Photosystem II reaction center protein X
    Species: Thermosynechococcus vulcanus [TaxId:32053]
    Database cross-references and differences (RAF-indexed):
    • Uniprot D0VWR4 (1-End)
      • initiating methionine (0)
  • 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):
  • Heterogens: OEX, FE2, CL, BCT, CLA, PHO, BCR, PL9, SQD, LMG, GOL, LMT, LHG, PG4, PGE, P6G, EDO, CA, HTG, 1PE, DGD, HEM, MG, HEC, 2PE, PE8, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5v2cA (A:)
mtttlqrresanlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdi
dgirepvsgsllygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfl
lgascymgrqwelsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtf
nfmivfqaehnilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfg
qeeetynivaahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngf
nfnhsvidakgnvintwadiinranlgmevmhernahnfpldla

    Sequence, based on observed residues (ATOM records): (download) 
    >5v2cA (A:)
anlwerfcnwvtstdnrlyvgwfgvimiptllaaticfviafiaappvdidgirepvsgs
llygnniitgavvpssnaiglhfypiweaasldewlynggpyqliifhfllgascymgrq
welsyrlgmrpwicvaysaplasafavfliypigqgsfsdgmplgisgtfnfmivfqaeh
nilmhpfhqlgvagvfggalfcamhgslvtsslirettetesanygykfgqeeetyniva
ahgyfgrlifqyasfnnsrslhfflaawpvvgvwfaalgistmafnlngfnfnhsvidak
gnvintwadiinranlgmevmhernahnfpldla

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5v2cB (B:)
glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
idpelspeqvewgfyqkvgdvttrsd

    Sequence, based on observed residues (ATOM records): (download) 
    >5v2cB (B:)
glpwyrvhtvlindpgrliaahlmhtalvagwagsmalyelatfdpsdpvlnpmwrqgmf
vlpfmarlgvtgswsgwsitgetgidpgfwsfegvalahivlsgllflaacwhwvywdle
lfrdprtgepaldlpkmfgihlflagllcfgfgafhltglfgpgmwvsdpygltgsvqpv
apewgpdgfnpynpggvvahhiaagivgiiaglfhilvrppqrlykalrmgnietvlsss
iaavffaafvvagtmwygsattpielfgptryqwdssyfqqeinrrvqaslasgatleea
wsaipeklafydyignnpakgglfrtgpmnkgdgiaqawkghavfrnkegeelfvrrmpa
ffesfpviltdkngvvkadipfrraeskysfeqqgvtvsfyggelngqtftdpptvksya
rkaifgeifefdtetlnsdgifrtsprgwftfahavfallfffghiwhgartlfrdvfsg
idpelspeqvewgfyqkvgdvttr

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5v2cC (C:)
eaansifatnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfelahf
ipekpmyeqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyhair
gpetleeyssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapgggd
vrvitnptldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhiltt
pfgwarrafiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqaqam
tflirdqklganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgpngl
dlnkikndiqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfvlaf
fflvghlwhagraraaaagfekgidresepvlsmpsld

    Sequence, based on observed residues (ATOM records): (download) 
    >5v2cC (C:)
atnrdqessgfawwagnarlinlsgkllgahvahaglivfwagamtlfelahfipekpmy
eqgliliphiatlgwgvgpggevvdtfpffvvgvvhlissavlgfggvyhairgpetlee
yssffgydwkdknkmttilgfhlivlgigalllvakamffgglydtwapgggdvrvitnp
tldprvifgyllkspfggegwivsvnnledvvgghiwigliciaggiwhilttpfgwarr
afiwsgeaylsyslgalsmmgfiatcfvwfnntvypsefygptgpeasqaqamtflirdq
klganvgsaqgptglgkylmrsptgeiifggetmrfwdfrgpwleplrgpngldlnkikn
diqpwqerraaeymthaplgslnsvggvateinsvnfvsprswlatshfvlaffflvghl
whagraraaaagfekgidresepvlsmpsld

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5v2cD (D:)
ergwfdilddwlkrdrfvfvgwsgillfpcaylalggwltgttfvtswythglassyleg
cnfltvavstpansmghsllllwgpeaqgdftrwcqlgglwtfialhgafgligfmlrqf
eiarlvgvrpynaiafsapiavfvsvfliyplgqsswffapsfgvaaifrfllffqgfhn
wtlnpfhmmgvagvlggallcaihgatventlfqdgegastfrafnptqaeetysmvtan
rfwsqifgiafsnkrwlhffmlfvpvtglwmsaigvvglalnlrsydfisqeiraaedpe
fetfytknlllnegirawmapqdqphenfvfpeevlprgnal

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >5v2cE (E:)
agttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeqr
siplvtdrfeakqqvetfleqlk

    Sequence, based on observed residues (ATOM records): (download) 
    >5v2cE (E:)
ttgerpfsdiitsvrywvihsitipalfiagwlfvstglaydvfgtprpdsyyaqeqrsi
plvtdrfeakqqvetfleqlk

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >5v2cF (F:)
tsntpnqepvsypiftvrwvavhtlavptifflgaiaamqfiqr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v2cF (F:)
sypiftvrwvavhtlavptifflgaiaamqfiqr

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5v2cH (H:)
arrtwlgdilrplnseygkvapgwgttplmavfmglflvflliileiynstlildgvnvs
wkalg

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5v2cI (I:)
metlkitvyivvtffvllfvfgflsgdparnpkrkdle

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >5v2cJ (J:)
meseggriplwivatvagmgvivivglffygayaglgssl

    Sequence, based on observed residues (ATOM records): (download) 
    >5v2cJ (J:)
eseggriplwivatvagmgvivivglffygayaglgssl

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5v2cK (K:)
klpeayaifdplvdvlpvipvlflalafvwqaavgfr

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5v2cL (L:)
mepnpnrqpvelnrtslylglllilvlallfssyffn

  • Chain 'M':
    Sequence, based on SEQRES records: (download) 
    >5v2cM (M:)
mevnqlgliatalfvlvpsvfliilyvqtesqqkss

    Sequence, based on observed residues (ATOM records): (download) 
    >5v2cM (M:)
mevnqlgliatalfvlvpsvfliilyvqtesqqk

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5v2cO (O:)
aatltyddivgtglankcptlddtargaypidssqtyriarlclqpttflvkeepknkrq
eaefvptklvtrettsldqiqgelkvnsdgsltfveedgidfqpvtvqmaggeripllft
vknlvastqpnvtsittstdfkgefnvpsyrtanfldpkgrglasgydsaialpqakeee
laranvkrfsltkgqislnvakvdgrtgeiagtfeseqlsdddmgahephevkiqgvfya
siepa

  • Chain 'T':
    Sequence, based on SEQRES records: (download) 
    >5v2cT (T:)
metityvfifaciialfffaiffreppritkk

    Sequence, based on observed residues (ATOM records): (download) 
    >5v2cT (T:)
metityvfifaciialfffaiffrepprit

  • Chain 'U':
    Sequence, based on SEQRES records: (download) 
    >5v2cU (U:)
atasteeelvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesved
vlnipglterqkqilrenlehftvtevetalveggdrynnglyk

    Sequence, based on observed residues (ATOM records): (download) 
    >5v2cU (U:)
elvnvvdeklgtaygekidlnntniaafiqyrglyptlaklivknapyesvedvlnipgl
terqkqilrenlehftvtevetalveggdrynnglyk

  • Chain 'V':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5v2cV (V:)
aeltpevltvplnsegktitltekqylegkrlfqyacaschvggitktnpsldlrtetla
latpprdnieglvdymknpttydgeqeiaevhpslrsadifpkmrnltekdlvaiaghil
vepkilgdkwgggkvyy

  • Chain 'X':
    Sequence, based on SEQRES records: (download) 
    >5v2cX (X:)
mtitpslkgffigllsgavvlgltfavliaisqidkvqrsl

    Sequence, based on observed residues (ATOM records): (download) 
    >5v2cX (X:)
mtitpslkgffigllsgavvlgltfavliaisqidkvqrs

  • Chain 'Y':
    No sequence available.

  • Chain 'Z':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5v2cZ (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':
    No sequence available.

  • Chain 'h':
    No sequence available.

  • Chain 'i':
    No sequence available.

  • Chain 'j':
    No sequence available.

  • 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':
    No sequence available.

  • Chain 'x':
    No sequence available.

  • Chain 'y':
    No sequence available.

  • Chain 'z':
    No sequence available.