PDB entry 1yq9

View 1yq9 on RCSB PDB site
Description: Structure of the unready oxidized form of [NiFe] hydrogenase
Class: oxidoreductase
Keywords: oxidoreductase
Deposited on 2005-02-01, released 2005-04-19
The last revision prior to the SCOPe 2.08 freeze date was dated 2017-10-11, with a file datestamp of 2017-10-06.
Experiment type: XRAY
Resolution: 2.35 Å
R-factor: N/A
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Periplasmic [NiFe] hydrogenase Small subunit
    Species: Desulfovibrio gigas [TaxId:879]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P12943 (Start-263)
      • see remark 999 (23)
      • see remark 999 (88)
    Domains in SCOPe 2.08: d1yq9a_
  • Chain 'B':
    Compound: Periplasmic [NiFe] hydrogenase Small subunit
    Species: Desulfovibrio gigas [TaxId:879]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P12943 (Start-263)
      • see remark 999 (23)
      • see remark 999 (88)
    Domains in SCOPe 2.08: d1yq9b_
  • Chain 'H':
    Compound: Periplasmic [NiFe] hydrogenase Large subunit
    Species: Desulfovibrio gigas [TaxId:879]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P12944 (Start-535)
      • see remark 999 (481)
      • see remark 999 (496)
    Domains in SCOPe 2.08: d1yq9h1
  • Chain 'I':
    Compound: Periplasmic [NiFe] hydrogenase Large subunit
    Species: Desulfovibrio gigas [TaxId:879]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P12944 (Start-535)
      • see remark 999 (481)
      • see remark 999 (496)
    Domains in SCOPe 2.08: d1yq9i_
  • Heterogens: SF4, F3S, H2S, GOL, NI, MG, FCO, PER, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >1yq9A (A:)
ltakkrpsvvylhnaectgcsesvlrtvdpyvdelildvismdyhetlmagaghaveeal
heaikgdfvcvieggipmgdggywgkvggrnmydicaevapkakaviaigtcatyggvqa
akpnptgtvgvnealgklgvkainiagcppnpmnfvgtvvhlltkgmpeldkqgrpvmff
getvhdncprlkhfeagefatsfgspeakkgyclyelgckgpdtynncpkqlfnqvnwpv
qaghpciacsepnfwdlyspfysa

    Sequence, based on observed residues (ATOM records): (download) 
    >1yq9A (A:)
kkrpsvvylhnaectgcsesvlrtvdpyvdelildvismdyhetlmagaghaveealhea
ikgdfvcvieggipmgdggywgkvggrnmydicaevapkakaviaigtcatyggvqaakp
nptgtvgvnealgklgvkainiagcppnpmnfvgtvvhlltkgmpeldkqgrpvmffget
vhdncprlkhfeagefatsfgspeakkgyclyelgckgpdtynncpkqlfnqvnwpvqag
hpciacsepnfwdlyspfysa

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >1yq9B (B:)
ltakkrpsvvylhnaectgcsesvlrtvdpyvdelildvismdyhetlmagaghaveeal
heaikgdfvcvieggipmgdggywgkvggrnmydicaevapkakaviaigtcatyggvqa
akpnptgtvgvnealgklgvkainiagcppnpmnfvgtvvhlltkgmpeldkqgrpvmff
getvhdncprlkhfeagefatsfgspeakkgyclyelgckgpdtynncpkqlfnqvnwpv
qaghpciacsepnfwdlyspfysa

    Sequence, based on observed residues (ATOM records): (download) 
    >1yq9B (B:)
krpsvvylhnaectgcsesvlrtvdpyvdelildvismdyhetlmagaghaveealheai
kgdfvcvieggipmgdggywgkvggrnmydicaevapkakaviaigtcatyggvqaakpn
ptgtvgvnealgklgvkainiagcppnpmnfvgtvvhlltkgmpeldkqgrpvmffgetv
hdncprlkhfeagefatsfgspeakkgyclyelgckgpdtynncpkqlfnqvnwpvqagh
pciacsepnfwdlyspfysa

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >1yq9H (H:)
msemqgnkivvdpitrieghlrieveveggkiknawsmstlfrglemilkgrdprdaqhf
tqracgvctyvhalasvravdncvgvkipenatlmrnltmgaqymhdhlvhfyhlhaldw
vnvanalnadpakaarlandlsprkttteslkavqakvkalvesgqlgiftnayflgghp
ayvlpaevdliatahylealrvqvkaaramaifgaknphtqftvvggctnydslrperia
efrklykevrefieqvyitdllavagfyknwagigktsnfltcgefptdeydlnsrytpq
gviwgndlskvddfnpdlieehvkyswyegadahhpykgvtkpkwtefhgedryswmkap
rykgeafevgplasvlvayakkheptvkavdlvlktlgvgpealfstlgrtaargiqclt
aaqevevwldkleanvkagkddlytdwqyptesqgvgfvnaprgmlshwivqrggkienf
qlvvpstwnlgprcaegklsaveqaligtpiadpkrpveilrtvhsydpciacgvh

    Sequence, based on observed residues (ATOM records): (download) 
    >1yq9H (H:)
nkivvdpitrieghlrieveveggkiknawsmstlfrglemilkgrdprdaqhftqracg
vctyvhalasvravdncvgvkipenatlmrnltmgaqymhdhlvhfyhlhaldwvnvana
lnadpakaarlandlsprkttteslkavqakvkalvesgqlgiftnayflgghpayvlpa
evdliatahylealrvqvkaaramaifgaknphtqftvvggctnydslrperiaefrkly
kevrefieqvyitdllavagfyknwagigktsnfltcgefptdeydlnsrytpqgviwgn
dlskvddfnpdlieehvkyswyegadahhpykgvtkpkwtefhgedryswmkaprykgea
fevgplasvlvayakkheptvkavdlvlktlgvgpealfstlgrtaargiqcltaaqeve
vwldkleanvkagkddlytdwqyptesqgvgfvnaprgmlshwivqrggkienfqlvvps
twnlgprcaegklsaveqaligtpiadpkrpveilrtvhsydpciacgvh

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >1yq9I (I:)
msemqgnkivvdpitrieghlrieveveggkiknawsmstlfrglemilkgrdprdaqhf
tqracgvctyvhalasvravdncvgvkipenatlmrnltmgaqymhdhlvhfyhlhaldw
vnvanalnadpakaarlandlsprkttteslkavqakvkalvesgqlgiftnayflgghp
ayvlpaevdliatahylealrvqvkaaramaifgaknphtqftvvggctnydslrperia
efrklykevrefieqvyitdllavagfyknwagigktsnfltcgefptdeydlnsrytpq
gviwgndlskvddfnpdlieehvkyswyegadahhpykgvtkpkwtefhgedryswmkap
rykgeafevgplasvlvayakkheptvkavdlvlktlgvgpealfstlgrtaargiqclt
aaqevevwldkleanvkagkddlytdwqyptesqgvgfvnaprgmlshwivqrggkienf
qlvvpstwnlgprcaegklsaveqaligtpiadpkrpveilrtvhsydpciacgvh

    Sequence, based on observed residues (ATOM records): (download) 
    >1yq9I (I:)
nkivvdpitrieghlrieveveggkiknawsmstlfrglemilkgrdprdaqhftqracg
vctyvhalasvravdncvgvkipenatlmrnltmgaqymhdhlvhfyhlhaldwvnvana
lnadpakaarlandlsprkttteslkavqakvkalvesgqlgiftnayflgghpayvlpa
evdliatahylealrvqvkaaramaifgaknphtqftvvggctnydslrperiaefrkly
kevrefieqvyitdllavagfyknwagigktsnfltcgefptdeydlnsrytpqgviwgn
dlskvddfnpdlieehvkyswyegadahhpykgvtkpkwtefhgedryswmkaprykgea
fevgplasvlvayakkheptvkavdlvlktlgvgpealfstlgrtaargiqcltaaqeve
vwldkleanvkagkddlytdwqyptesqgvgfvnaprgmlshwivqrggkienfqlvvps
twnlgprcaegklsaveqaligtpiadpkrpveilrtvhsydpciacgvh