PDB entry 4ud2

View 4ud2 on RCSB PDB site
Description: Structure of anaerobically purified D. fructosovorans NiFe- hydrogenase
Class: oxidoreductase
Keywords: oxidoreductase, ni-sib state, ni-c state
Deposited on 2014-12-05, released 2015-03-25
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-03-06, with a file datestamp of 2019-03-01.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: N/A
AEROSPACI score: 0.25 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Hydrogenase (NiFe) small subunit HydA
    Species: DESULFOVIBRIO FRUCTOSIVORANS JJ [TaxId:596151]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ud2a_
  • Chain 'B':
    Compound: Hydrogenase (NiFe) small subunit HydA
    Species: DESULFOVIBRIO FRUCTOSIVORANS JJ [TaxId:596151]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ud2b_
  • Chain 'C':
    Compound: Hydrogenase (NiFe) small subunit HydA
    Species: DESULFOVIBRIO FRUCTOSIVORANS JJ [TaxId:596151]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ud2c_
  • Chain 'Q':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: DESULFOVIBRIO FRUCTOSIVORANS JJ [TaxId:596151]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ud2q_
  • Chain 'R':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: DESULFOVIBRIO FRUCTOSIVORANS JJ [TaxId:596151]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ud2r_
  • Chain 'S':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: DESULFOVIBRIO FRUCTOSIVORANS JJ [TaxId:596151]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ud2s_
  • Heterogens: GOL, SF4, F3S, FCO, NI, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4ud2A (A:)
ltakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaal
hqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggv
qkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfyg
elvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvq
aghpclgcsepdfwdtmtpfyeqg

    Sequence, based on observed residues (ATOM records): (download) 
    >4ud2A (A:)
akhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaalhq
alegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggvqk
akpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfygel
vhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvqag
hpclgcsepdfwdtmtpfyeqg

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >4ud2B (B:)
ltakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaal
hqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggv
qkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfyg
elvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvq
aghpclgcsepdfwdtmtpfyeqg

    Sequence, based on observed residues (ATOM records): (download) 
    >4ud2B (B:)
akhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaalhq
alegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggvqk
akpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfygel
vhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvqag
hpclgcsepdfwdtmtpfyeqg

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >4ud2C (C:)
ltakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaal
hqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggv
qkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfyg
elvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvq
aghpclgcsepdfwdtmtpfyeqg

    Sequence, based on observed residues (ATOM records): (download) 
    >4ud2C (C:)
hrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaalhqal
egkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggvqkak
pnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfygelvh
dncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvqaghp
clgcsepdfwdtmtpfyeqg

  • Chain 'Q':
    Sequence, based on SEQRES records: (download) 
    >4ud2Q (Q:)
maeskptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrd
prdaqhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfy
hlhaldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgift
nayflgghkayylppevdliatahylealhmqvkaasamailggknphtqftvvggcsny
qgltkdplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatdds
spekhlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkyt
klddkdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhs
tlgrtaargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgals
hwirikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhaf
dpciacgvh

    Sequence, based on observed residues (ATOM records): (download) 
    >4ud2Q (Q:)
ptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprdaq
hftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlhal
dwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayfl
gghkayylppevdliatahylealhmqvkaasamailggknphtqftvvggcsnyqgltk
dplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspekh
latsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytklddk
dhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgrt
aargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwiri
kgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpcia
cgvh

  • Chain 'R':
    Sequence, based on SEQRES records: (download) 
    >4ud2R (R:)
maeskptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrd
prdaqhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfy
hlhaldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgift
nayflgghkayylppevdliatahylealhmqvkaasamailggknphtqftvvggcsny
qgltkdplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatdds
spekhlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkyt
klddkdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhs
tlgrtaargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgals
hwirikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhaf
dpciacgvh

    Sequence, based on observed residues (ATOM records): (download) 
    >4ud2R (R:)
ptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprdaq
hftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlhal
dwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayfl
gghkayylppevdliatahylealhmqvkaasamailggknphtqftvvggcsnyqgltk
dplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspekh
latsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytklddk
dhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgrt
aargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwiri
kgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpcia
cgvh

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >4ud2S (S:)
maeskptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrd
prdaqhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfy
hlhaldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgift
nayflgghkayylppevdliatahylealhmqvkaasamailggknphtqftvvggcsny
qgltkdplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatdds
spekhlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkyt
klddkdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhs
tlgrtaargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgals
hwirikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhaf
dpciacgvh

    Sequence, based on observed residues (ATOM records): (download) 
    >4ud2S (S:)
ptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprdaq
hftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlhal
dwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayfl
gghkayylppevdliatahylealhmqvkaasamailggknphtqftvvggcsnyqgltk
dplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspekh
latsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytklddk
dhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgrt
aargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwiri
kgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpcia
cgvh