PDB entry 1yqw

View 1yqw on RCSB PDB site
Description: Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase
Class: oxidoreductase
Keywords: ni-fe hydrogenase unready state, oxidoreductase
Deposited on 2005-02-02, released 2005-04-19
The last revision prior to the SCOPe 2.03 freeze date was dated 2011-08-31, with a file datestamp of 2011-08-26.
Experiment type: XRAY
Resolution: 1.83 Å
R-factor: 0.148
AEROSPACI score: 0.54 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Periplasmic [NiFe] hydrogenase Small subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d1yqwa_
  • Chain 'B':
    Compound: Periplasmic [NiFe] hydrogenase Small subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d1yqwb_
  • Chain 'C':
    Compound: Periplasmic [NiFe] hydrogenase Small subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d1yqwc_
  • Chain 'Q':
    Compound: Periplasmic [NiFe] hydrogenase Large subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P18188 (Start-548)
      • conflict (197)
      • conflict (302)
      • engineered mutation (498)
    Domains in SCOPe 2.03: d1yqwq_
  • Chain 'R':
    Compound: Periplasmic [NiFe] hydrogenase Large subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P18188 (Start-548)
      • conflict (197)
      • conflict (302)
      • engineered mutation (498)
    Domains in SCOPe 2.03: d1yqwr_
  • Chain 'S':
    Compound: Periplasmic [NiFe] hydrogenase Large subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P18188 (Start-548)
      • conflict (197)
      • conflict (302)
      • engineered mutation (498)
    Domains in SCOPe 2.03: d1yqws_
  • Heterogens: NI, FE2, BCT, MG, SF4, F3S, FCO, PER, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >1yqwA (A:)
ltakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaal
hqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggv
qkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfyg
elvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvq
aghpclgcsepdfwdtmtpfyeqg

    Sequence, based on observed residues (ATOM records): (download) 
    >1yqwA (A:)
akhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaalhq
alegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggvqk
akpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfygel
vhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvqag
hpclgcsepdfwdtmtpfyeqg

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >1yqwB (B:)
ltakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaal
hqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggv
qkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfyg
elvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvq
aghpclgcsepdfwdtmtpfyeqg

    Sequence, based on observed residues (ATOM records): (download) 
    >1yqwB (B:)
akhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaalhq
alegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggvqk
akpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfygel
vhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvqag
hpclgcsepdfwdtmtpfyeqg

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >1yqwC (C:)
ltakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaal
hqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggv
qkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfyg
elvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvq
aghpclgcsepdfwdtmtpfyeqg

    Sequence, based on observed residues (ATOM records): (download) 
    >1yqwC (C:)
hrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaalhqal
egkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggvqkak
pnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfygelvh
dncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvqaghp
clgcsepdfwdtmtpfyeqg

  • Chain 'Q':
    Sequence, based on SEQRES records: (download) 
    >1yqwQ (Q:)
maeskptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrd
prdaqhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfy
hlhaldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgift
nayflgghkayylppevnliatahylealhmqvkaasamailggknphtqftvvggcsny
qgltkdplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatdds
spskhlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkyt
klddkdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhs
tlgrtaargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgals
hwirikgkkidnfqlvvpatwnlgprgaqgdkspveealigtpiadpkrpveilrtvhaf
dpciacgvh

    Sequence, based on observed residues (ATOM records): (download) 
    >1yqwQ (Q:)
ptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprdaq
hftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlhal
dwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayfl
gghkayylppevnliatahylealhmqvkaasamailggknphtqftvvggcsnyqgltk
dplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspskh
latsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytklddk
dhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgrt
aargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwiri
kgkkidnfqlvvpatwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpcia
cgvh

  • Chain 'R':
    Sequence, based on SEQRES records: (download) 
    >1yqwR (R:)
maeskptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrd
prdaqhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfy
hlhaldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgift
nayflgghkayylppevnliatahylealhmqvkaasamailggknphtqftvvggcsny
qgltkdplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatdds
spskhlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkyt
klddkdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhs
tlgrtaargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgals
hwirikgkkidnfqlvvpatwnlgprgaqgdkspveealigtpiadpkrpveilrtvhaf
dpciacgvh

    Sequence, based on observed residues (ATOM records): (download) 
    >1yqwR (R:)
kptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprda
qhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlha
ldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayf
lgghkayylppevnliatahylealhmqvkaasamailggknphtqftvvggcsnyqglt
kdplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspsk
hlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytkldd
kdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgr
taargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwir
ikgkkidnfqlvvpatwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpci
acgvh

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >1yqwS (S:)
maeskptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrd
prdaqhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfy
hlhaldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgift
nayflgghkayylppevnliatahylealhmqvkaasamailggknphtqftvvggcsny
qgltkdplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatdds
spskhlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkyt
klddkdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhs
tlgrtaargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgals
hwirikgkkidnfqlvvpatwnlgprgaqgdkspveealigtpiadpkrpveilrtvhaf
dpciacgvh

    Sequence, based on observed residues (ATOM records): (download) 
    >1yqwS (S:)
ptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprdaq
hftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlhal
dwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayfl
gghkayylppevnliatahylealhmqvkaasamailggknphtqftvvggcsnyqgltk
dplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspskh
latsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytklddk
dhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgrt
aargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwiri
kgkkidnfqlvvpatwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpcia
cgvh