PDB entry 7ddq

View 7ddq on RCSB PDB site
Description: Structure of RC-LH1-PufX from Rhodobacter veldkampii
Class: photosynthesis
Keywords: membrane protein, light-harvesting, reaction center, pufx, PHOTOSYNTHESIS
Deposited on 2020-10-29, released 2021-06-30
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-07-07, with a file datestamp of 2021-07-02.
Experiment type: EM
Resolution: 2.84 Å
R-factor: N/A
AEROSPACI score: 0.24 (click here for full SPACI score report)

Chains and heterogens:

• Chain 'A':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
• Chain 'B':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
  Domains in SCOPe 2.08: d7ddqb_
• Chain 'D':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
• Chain 'E':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
  Domains in SCOPe 2.08: d7ddqe_
• Chain 'F':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
  Domains in SCOPe 2.08: d7ddqf_
• Chain 'G':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
• Chain 'H':
  Compound: Photosynthetic reaction center subunit H
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIP4 (0-251)
  Domains in SCOPe 2.08: d7ddqh1, d7ddqh2
• Chain 'I':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
  Domains in SCOPe 2.08: d7ddqi_
• Chain 'J':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
  Domains in SCOPe 2.08: d7ddqj_
• Chain 'K':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
  Domains in SCOPe 2.08: d7ddqk_
• Chain 'L':
  Compound: Photosynthetic reaction center L subunit
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIS6 (0-275)
  Domains in SCOPe 2.08: d7ddql_
• Chain 'M':
  Compound: reaction center protein m chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIN0 (0-307)
  Domains in SCOPe 2.08: d7ddqm_
• Chain 'N':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
• Chain 'O':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
• Chain 'R':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
  Domains in SCOPe 2.08: d7ddqr_
• Chain 'S':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
• Chain 'T':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
• Chain 'U':
  Compound: Antenna pigment protein beta chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIL7 (0-47)
• Chain 'X':
  Compound: PufX
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIP3 (0-82)
• Chain 'a':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
  Domains in SCOPe 2.08: d7ddqa_
• Chain 'b':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
• Chain 'd':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
  Domains in SCOPe 2.08: d7ddqd_
• Chain 'e':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
• Chain 'f':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
• Chain 'g':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
  Domains in SCOPe 2.08: d7ddqg_
• Chain 'i':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
• Chain 'j':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
• Chain 'k':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
• Chain 'n':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
  Domains in SCOPe 2.08: d7ddqn_
• Chain 'o':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
  Domains in SCOPe 2.08: d7ddqo_
• Chain 'r':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
• Chain 's':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
  Domains in SCOPe 2.08: d7ddqs_
• Chain 't':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
  Domains in SCOPe 2.08: d7ddqt_
• Chain 'u':
  Compound: Antenna pigment protein alpha chain
  Species: Rhodobacter veldkampii DSM 11550 [TaxId:1185920]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A2T4JIR4 (0-56)
  Domains in SCOPe 2.08: d7ddqu_
• Heterogens: BCL, SPO, U10, BPH, FE, 3PE

PDB Chain Sequences:

• Chain 'A':
  No sequence available.
  
  
• Chain 'B':
  Sequence, based on SEQRES records: (download)
  

  >7ddqB (B:)
  madkdlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

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

  >7ddqB (B:)
  dlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

  
  
• Chain 'D':
  No sequence available.
  
  
• Chain 'E':
  Sequence, based on SEQRES records: (download)
  

  >7ddqE (E:)
  madkdlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

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

  >7ddqE (E:)
  dlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

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

  >7ddqF (F:)
  madkdlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

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

  >7ddqF (F:)
  dlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

  
  
• Chain 'G':
  No sequence available.
  
  
• Chain 'H':
  Sequence, based on SEQRES records: (download)
  

  >7ddqH (H:)
  mvgvnffgdfdlaslaiwsfwlffallvyylqtenmregyplenedggpavnqgpfplps
  qktfklphgrgevtvpdykkeardvalartavndgfphaptgnpmldgvgpaswaprrdi
  peldghghakvvpmsvasaffvsagrdprglpviandmktvgtvtemwvdvaehmvryle
  vdlasggkclvpmtmaiikkhavvvqsissaafasvpqtksmteismleeekicayfagg
  tmycadakpklf
  

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

  >7ddqH (H:)
  mvgvnffgdfdlaslaiwsfwlffallvyylqtenmregyplenedggpavnqgpfplps
  qktfklphgrgevtvpdykkeardvalartavndgfphaptgnpmldgvgpaswaprrdi
  peldghghakvvpmsvasaffvsagrdprglpviandmktvgtvtemwvdvaehmvryle
  vdlasggkclvpmtmaiikkhavvvqsissaafasvpqtksmteismleeekicayfagg
  tmycadakpk
  

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

  >7ddqI (I:)
  madkdlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

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

  >7ddqI (I:)
  dlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

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

  >7ddqJ (J:)
  madkdlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

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

  >7ddqJ (J:)
  dlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

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

  >7ddqK (K:)
  madkdlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

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

  >7ddqK (K:)
  dlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

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

  >7ddqL (L:)
  mallsferkyrvpggtliggnlfdfwvgpfyvgffgvtsvffaalgtlmilwgaslgdtw
  npllisinpppleyglgaaplreggiwqvvtlcaigafvswamreveicrklgiglhipf
  afsfaifayitlvvirpalmgawghgfqygvfthlewvnnvgyqygnfhynplhmlgisl
  fftttlalglhgalilsaanpetgkemrtpdhedtffrdlvgysvgtlgihrlglllaln
  aafwsamcilasgtvwfdqwvfwwdwwynlpfwadl
  

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

  >7ddqL (L:)
  allsferkyrvpggtliggnlfdfwvgpfyvgffgvtsvffaalgtlmilwgaslgdtwn
  pllisinpppleyglgaaplreggiwqvvtlcaigafvswamreveicrklgiglhipfa
  fsfaifayitlvvirpalmgawghgfqygvfthlewvnnvgyqygnfhynplhmlgislf
  ftttlalglhgalilsaanpetgkemrtpdhedtffrdlvgysvgtlgihrlglllalna
  afwsamcilasgtvwfdqwvfwwdwwynlpfwadl
  

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

  >7ddqM (M:)
  maeyqniftqvqvagkpelgmvegvnlenrttgttnwpilgwfgnaqlgpiylgtlgtms
  lifgafwfflvgvsfiiqadyspalflrelfraglfppapeyglslsaplmegglwlias
  fflmlsvllwwartykraadlgmgkhtawafagalwlmfvlsffrpilmgswseavpygi
  fphldwtnnfslthgnlfynpfhglsiaflygstmlfamhgatilavsrlggereleqiv
  drgtaaeraalfwrwtmgfnatmegihrwgwwfavltpvtggigillsgtvvedwsvwaq
  vhgykaln
  

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

  >7ddqM (M:)
  eyqniftqvqvagkpelgmvegvnlenrttgttnwpilgwfgnaqlgpiylgtlgtmsli
  fgafwfflvgvsfiiqadyspalflrelfraglfppapeyglslsaplmegglwliasff
  lmlsvllwwartykraadlgmgkhtawafagalwlmfvlsffrpilmgswseavpygifp
  hldwtnnfslthgnlfynpfhglsiaflygstmlfamhgatilavsrlggereleqivdr
  gtaaeraalfwrwtmgfnatmegihrwgwwfavltpvtggigillsgtvvedwsvwaqvh
  gykal
  

  
  
• Chain 'N':
  No sequence available.
  
  
• Chain 'O':
  No sequence available.
  
  
• Chain 'R':
  Sequence, based on SEQRES records: (download)
  

  >7ddqR (R:)
  madkdlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

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

  >7ddqR (R:)
  dlsftgltdqqaqelhsvylqgmwlfisvaivahlavfiwrpwl
  

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

  >7ddqa (a:)
  mskfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyervaae
  

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

  >7ddqa (a:)
  skfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwld
  

  
  
• Chain 'b':
  No sequence available.
  
  
• Chain 'd':
  Sequence, based on SEQRES records: (download)
  

  >7ddqd (d:)
  mskfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyervaae
  

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

  >7ddqd (d:)
  skfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyerv
  

  
  
• Chain 'e':
  No sequence available.
  
  
• Chain 'f':
  No sequence available.
  
  
• Chain 'g':
  Sequence, based on SEQRES records: (download)
  

  >7ddqg (g:)
  mskfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyervaae
  

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

  >7ddqg (g:)
  skfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyerv
  

  
  
• Chain 'i':
  No sequence available.
  
  
• Chain 'j':
  No sequence available.
  
  
• Chain 'k':
  No sequence available.
  
  
• Chain 'n':
  Sequence, based on SEQRES records: (download)
  

  >7ddqn (n:)
  mskfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyervaae
  

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

  >7ddqn (n:)
  skfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyerv
  

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

  >7ddqo (o:)
  mskfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyervaae
  

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

  >7ddqo (o:)
  skfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyerv
  

  
  
• Chain 'r':
  No sequence available.
  
  
• Chain 's':
  Sequence, based on SEQRES records: (download)
  

  >7ddqs (s:)
  mskfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyervaae
  

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

  >7ddqs (s:)
  skfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyerv
  

  
  
• Chain 't':
  Sequence, based on SEQRES records: (download)
  

  >7ddqt (t:)
  mskfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyervaae
  

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

  >7ddqt (t:)
  skfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyerv
  

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

  >7ddqu (u:)
  mskfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyervaae
  

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

  >7ddqu (u:)
  kfykiwlifdprrvfvaqgvflfllavmihlmllsnpgfnwldisgvkyerv