PDB entry 5odi

View 5odi on RCSB PDB site
Description: Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus cocrystallized with CoM-SH
Class: oxidoreductase
Keywords: Heterodisulfide reductase, [NiFe]-hydrogenase, FeS cluster, ferredoxin, CCG motif, methanogenesis, flavoprotein, flavin-based electron bifurcation, [2Fe-2S] cluster, macromolecular complex, anaerobic, thioredoxin, metabolism, oxydoreductase., OXIDOREDUCTASE
Deposited on 2017-07-05, released 2017-08-30
The last revision prior to the SCOPe 2.08 freeze date was dated 2017-08-30, with a file datestamp of 2017-08-25.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: N/A
AEROSPACI score: 0.22 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Heterodisulfide reductase, subunit A
    Species: Methanothermococcus thermolithotrophicus DSM 2095 [TaxId:523845]
    Database cross-references and differences (RAF-indexed):
    • PDB 5ODI
  • Chain 'B':
    Compound: Heterodisulfide reductase, subunit B
    Species: Methanothermococcus thermolithotrophicus DSM 2095 [TaxId:523845]
    Database cross-references and differences (RAF-indexed):
    • PDB 5ODI (0-290)
  • Chain 'C':
    Compound: Heterodisulfide reductase, subunit C
    Species: Methanothermococcus thermolithotrophicus DSM 2095 [TaxId:523845]
    Database cross-references and differences (RAF-indexed):
    • PDB 5ODI (0-183)
  • Chain 'D':
    Compound: Methyl-viologen reducing hydrogenase, subunit D
    Species: Methanothermococcus thermolithotrophicus DSM 2095 [TaxId:523845]
    Database cross-references and differences (RAF-indexed):
    • PDB 5ODI (Start-139)
  • Chain 'E':
    Compound: Methyl-viologen reducing hydrogenase, subunit G
    Species: Methanothermococcus thermolithotrophicus DSM 2095 [TaxId:523845]
    Database cross-references and differences (RAF-indexed):
    • PDB 5ODI
  • Chain 'F':
    Compound: Methyl-viologen reducing hydrogenase, subunit A
    Species: Methanothermococcus thermolithotrophicus DSM 2095 [TaxId:523845]
    Database cross-references and differences (RAF-indexed):
    • PDB 5ODI
    Domains in SCOPe 2.08: d5odif_
  • Chain 'G':
    Compound: Heterodisulfide reductase, subunit A
    Species: Methanothermococcus thermolithotrophicus DSM 2095 [TaxId:523845]
    Database cross-references and differences (RAF-indexed):
    • PDB 5ODI
  • Chain 'H':
    Compound: Heterodisulfide reductase, subunit B
    Species: Methanothermococcus thermolithotrophicus DSM 2095 [TaxId:523845]
    Database cross-references and differences (RAF-indexed):
    • PDB 5ODI (0-290)
  • Chain 'I':
    Compound: Heterodisulfide reductase, subunit C
    Species: Methanothermococcus thermolithotrophicus DSM 2095 [TaxId:523845]
    Database cross-references and differences (RAF-indexed):
    • PDB 5ODI (0-End)
  • Chain 'J':
    Compound: Methyl-viologen reducing hydrogenase, subunit D
    Species: Methanothermococcus thermolithotrophicus DSM 2095 [TaxId:523845]
    Database cross-references and differences (RAF-indexed):
    • PDB 5ODI (Start-139)
  • Chain 'K':
    Compound: Methyl-viologen reducing hydrogenase, subunit G
    Species: Methanothermococcus thermolithotrophicus DSM 2095 [TaxId:523845]
    Database cross-references and differences (RAF-indexed):
    • PDB 5ODI
  • Chain 'L':
    Compound: Methyl-viologen reducing hydrogenase, subunit A
    Species: Methanothermococcus thermolithotrophicus DSM 2095 [TaxId:523845]
    Database cross-references and differences (RAF-indexed):
    • PDB 5ODI
    Domains in SCOPe 2.08: d5odil_
  • Heterogens: ACT, FAD, SF4, GOL, 9S8, COM, FES, TRS, NFU, FE, PE3, 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) 
    >5odiF (F:)
mvklsvepvtrveghgkisvsfddsgnldkvrfhvvevrgfekflegryvedapiytpri
cgicqvahhlasakavdnvfgvkipetaellrnlmhqgatvhshalhfymlaapdlmfpt
tddvlkrnlmgiakehpeiikdaielrkagqnvvrvvggraihpvtavvggqskslkeee
rdellklsertielseksievgkkllenikdedlldigyfesahmgmvnngvhdlydgkl
rvvnsegkveyefdpseymnyiaegvkpysylkfpylkdkgeedgiyrvntlsrlnvsdk
matplaqkyydefvkefgkpchhpmlfhyarliellssaemvkellendkivgediraep
eevvgdgvgcveaprgtlihhfktdddgiitdtnlvvatvqnnpamdigvrkvaekyika
pedatpqvlnymemliraydpclscathiigeesnnlsldvyqknklvksirg

    Sequence, based on observed residues (ATOM records): (download) 
    >5odiF (F:)
vklsvepvtrveghgkisvsfddsgnldkvrfhvvevrgfekflegryvedapiytpric
gicqvahhlasakavdnvfgvkipetaellrnlmhqgatvhshalhfymlaapdlmfptt
ddvlkrnlmgiakehpeiikdaielrkagqnvvrvvggraihpvtavvggqskslkeeer
dellklsertielseksievgkkllenikdedlldigyfesahmgmvnngvhdlydgklr
vvnsegkveyefdpseymnyiaegvkpysylkfpylkdkgeedgiyrvntlsrlnvsdkm
atplaqkyydefvkefgkpchhpmlfhyarliellssaemvkellendkivgediraepe
evvgdgvgcveaprgtlihhfktdddgiitdtnlvvatvqnnpamdigvrkvaekyikap
edatpqvlnymemliraydpclscath

  • Chain 'G':
    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':
    Sequence, based on SEQRES records: (download) 
    >5odiL (L:)
mvklsvepvtrveghgkisvsfddsgnldkvrfhvvevrgfekflegryvedapiytpri
cgicqvahhlasakavdnvfgvkipetaellrnlmhqgatvhshalhfymlaapdlmfpt
tddvlkrnlmgiakehpeiikdaielrkagqnvvrvvggraihpvtavvggqskslkeee
rdellklsertielseksievgkkllenikdedlldigyfesahmgmvnngvhdlydgkl
rvvnsegkveyefdpseymnyiaegvkpysylkfpylkdkgeedgiyrvntlsrlnvsdk
matplaqkyydefvkefgkpchhpmlfhyarliellssaemvkellendkivgediraep
eevvgdgvgcveaprgtlihhfktdddgiitdtnlvvatvqnnpamdigvrkvaekyika
pedatpqvlnymemliraydpclscathiigeesnnlsldvyqknklvksirg

    Sequence, based on observed residues (ATOM records): (download) 
    >5odiL (L:)
vklsvepvtrveghgkisvsfddsgnldkvrfhvvevrgfekflegryvedapiytpric
gicqvahhlasakavdnvfgvkipetaellrnlmhqgatvhshalhfymlaapdlmfptt
ddvlkrnlmgiakehpeiikdaielrkagqnvvrvvggraihpvtavvggqskslkeeer
dellklsertielseksievgkkllenikdedlldigyfesahmgmvnngvhdlydgklr
vvnsegkveyefdpseymnyiaegvkpysylkfpylkdkgeedgiyrvntlsrlnvsdkm
atplaqkyydefvkefgkpchhpmlfhyarliellssaemvkellendkivgediraepe
evvgdgvgcveaprgtlihhfktdddgiitdtnlvvatvqnnpamdigvrkvaekyikap
edatpqvlnymemliraydpclscath