PDB entry 1yrq

View 1yrq on RCSB PDB site
Description: Structure of the ready oxidized form of [NiFe]-hydrogenase
Class: oxidoreductase
Keywords: NiB state, hydroxide bridge, Oxidoreductase
Deposited on 2005-02-04, released 2005-04-19
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-10-11, with a file datestamp of 2017-10-06.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: N/A
AEROSPACI score: 0.28 (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):
    • Uniprot P18187 (Start-263)
      • conflict (170)
    Domains in SCOPe 2.07: d1yrqa_
  • Chain 'B':
    Compound: Periplasmic [NiFe] hydrogenase Small subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P18187 (Start-263)
      • conflict (170)
    Domains in SCOPe 2.07: d1yrqb_
  • Chain 'C':
    Compound: Periplasmic [NiFe] hydrogenase Small subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P18187 (Start-263)
      • conflict (170)
    Domains in SCOPe 2.07: d1yrqc_
  • Chain 'D':
    Compound: Periplasmic [NiFe] hydrogenase Small subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P18187 (Start-263)
      • conflict (170)
    Domains in SCOPe 2.07: d1yrqd_
  • Chain 'F':
    Compound: Periplasmic [NiFe] hydrogenase Small subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P18187 (Start-263)
      • conflict (170)
    Domains in SCOPe 2.07: d1yrqf_
  • Chain 'G':
    Compound: Periplasmic [NiFe] hydrogenase Small subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P18187 (Start-263)
      • conflict (170)
    Domains in SCOPe 2.07: d1yrqg_
  • Chain 'H':
    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)
    Domains in SCOPe 2.07: d1yrqh_
  • Chain 'I':
    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)
    Domains in SCOPe 2.07: d1yrqi_
  • Chain 'J':
    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)
    Domains in SCOPe 2.07: d1yrqj_
  • Chain 'K':
    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)
    Domains in SCOPe 2.07: d1yrqk_
  • Chain 'M':
    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)
    Domains in SCOPe 2.07: d1yrqm_
  • Chain 'N':
    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)
    Domains in SCOPe 2.07: d1yrqn_
  • Heterogens: SF4, F3S, NI, MG, FCO, HOH

PDB Chain Sequences:

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

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

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

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

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

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

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >1yrqD (D:)
ltakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaal
hqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggv
qkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldsngrpklfyg
elvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvq
aghpclgcsepdfwdtmtpfyeqg

    Sequence, based on observed residues (ATOM records): (download) 
    >1yrqD (D:)
akhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaalhq
alegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggvqk
akpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldsngrpklfygel
vhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvqag
hpclgcsepdfwdtmtpfyeqg

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >1yrqF (F:)
ltakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaal
hqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggv
qkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldsngrpklfyg
elvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvq
aghpclgcsepdfwdtmtpfyeqg

    Sequence, based on observed residues (ATOM records): (download) 
    >1yrqF (F:)
hrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaalhqal
egkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggvqkak
pnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldsngrpklfygelvh
dncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvqaghp
clgcsepdfwdtmtpfyeqg

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >1yrqG (G:)
ltakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaal
hqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggv
qkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldsngrpklfyg
elvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvq
aghpclgcsepdfwdtmtpfyeqg

    Sequence, based on observed residues (ATOM records): (download) 
    >1yrqG (G:)
akhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaalhq
alegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggvqk
akpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldsngrpklfygel
vhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvqag
hpclgcsepdfwdtmtpfyeqg

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

    Sequence, based on observed residues (ATOM records): (download) 
    >1yrqH (H:)
kptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprda
qhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlha
ldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayf
lgghkayylppevnliatahylealhmqvkaasamailggknphtqftvvggcsnyqglt
kdplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspsk
hlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytkldd
kdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgr
taargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwir
ikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpci
acgvh

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

    Sequence, based on observed residues (ATOM records): (download) 
    >1yrqI (I:)
kptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprda
qhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlha
ldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayf
lgghkayylppevnliatahylealhmqvkaasamailggknphtqftvvggcsnyqglt
kdplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspsk
hlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytkldd
kdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgr
taargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwir
ikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpci
acgvh

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

    Sequence, based on observed residues (ATOM records): (download) 
    >1yrqJ (J:)
ptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprdaq
hftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlhal
dwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayfl
gghkayylppevnliatahylealhmqvkaasamailggknphtqftvvggcsnyqgltk
dplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspskh
latsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytklddk
dhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgrt
aargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwiri
kgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpcia
cgvh

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

    Sequence, based on observed residues (ATOM records): (download) 
    >1yrqK (K:)
ptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprdaq
hftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlhal
dwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayfl
gghkayylppevnliatahylealhmqvkaasamailggknphtqftvvggcsnyqgltk
dplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspskh
latsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytklddk
dhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgrt
aargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwiri
kgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpcia
cgvh

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

    Sequence, based on observed residues (ATOM records): (download) 
    >1yrqM (M:)
kptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprda
qhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlha
ldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayf
lgghkayylppevnliatahylealhmqvkaasamailggknphtqftvvggcsnyqglt
kdplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspsk
hlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytkldd
kdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgr
taargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwir
ikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpci
acgvh

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

    Sequence, based on observed residues (ATOM records): (download) 
    >1yrqN (N:)
kptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprda
qhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlha
ldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayf
lgghkayylppevnliatahylealhmqvkaasamailggknphtqftvvggcsnyqglt
kdplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspsk
hlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytkldd
kdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgr
taargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwir
ikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpci
acgvh