PDB entry 4urh

View 4urh on RCSB PDB site
Description: High-resolution structure of partially oxidized D. fructosovorans NiFe-hydrogenase
Class: oxidoreductase
Keywords: oxidoreductase, nife-site, ni-su state, sulfenate
Deposited on 2014-06-30, released 2014-10-29
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-02-27, with a file datestamp of 2019-02-22.
Experiment type: XRAY
Resolution: 1.44 Å
R-factor: N/A
AEROSPACI score: 0.51 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Hydrogenase (NiFe) small subunit HydA
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4urha_
  • Chain 'B':
    Compound: Hydrogenase (NiFe) small subunit HydA
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4urhb_
  • Chain 'C':
    Compound: Hydrogenase (NiFe) small subunit HydA
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4urhc_
  • Chain 'Q':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4urhq_
  • Chain 'R':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4urhr_
  • Chain 'S':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4urhs_
  • Heterogens: SF4, F3S, GOL, FCO, NI, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4urhA (A:)
altakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaa
lhqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsaygg
vqkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfy
gelvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpv
qaghpclgcsepdfwdtmtpfyeqg

    Sequence, based on observed residues (ATOM records): (download) 
    >4urhA (A:)
takhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaalh
qalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggvq
kakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfyge
lvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvqa
ghpclgcsepdfwdtmtpfyeqg

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >4urhB (B:)
altakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaa
lhqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsaygg
vqkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfy
gelvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpv
qaghpclgcsepdfwdtmtpfyeqg

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

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >4urhC (C:)
altakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaa
lhqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsaygg
vqkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfy
gelvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpv
qaghpclgcsepdfwdtmtpfyeqg

    Sequence, based on observed residues (ATOM records): (download) 
    >4urhC (C:)
ltakhrpsvvwlhnaectgcteaairtikpyidalildtisldyqetimaaageaaeaal
hqalegkdgyylvvegglptidggqwgmvaghpmiettkkaaakakgiicigtcsayggv
qkakpnpsqakgvsealgvktinipgcppnpinfvgavvhvltkgipdldengrpklfyg
elvhdncprlphfeasefapsfdseeakkgfclyelgckgpvtynncpkvlfnqvnwpvq
aghpclgcsepdfwdtmtpfyeqg

  • Chain 'Q':
    Sequence, based on SEQRES records: (download) 
    >4urhQ (Q:)
aswshpqfekgasgaaeskptpqstftgpivvdpitrieghlrimvevengkvkdawsss
qlfrgleiilkgrdprdaqhftqracgvctyvhalassrcvddavkvsipanarmmrnlv
masqylhdhlvhfyhlhaldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdk
lkafvesgqlgiftnayflgghkayylppevdliatahylealhmqvkaasamailggkn
phtqftvvggcsnyqgltknplanylalskevcqfvnecyipdllavagfykdwggiggt
snylafgefatddsspekhlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggd
gkhpydgvtdpkytklddkdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdm
vlgklsvpatalhstlgrtaargietaivcanmekwikemadsgakdntlcakwempees
kgvgladaprgalshwirikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiad
pkrpveilrtvhafdpciacgvh

    Sequence, based on observed residues (ATOM records): (download) 
    >4urhQ (Q:)
kptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprda
qhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlha
ldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayf
lgghkayylppevdliatahylealhmqvkaasamailggknphtqftvvggcsnyqglt
knplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspek
hlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytkldd
kdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgr
taargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwir
ikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpci
acgvh

  • Chain 'R':
    Sequence, based on SEQRES records: (download) 
    >4urhR (R:)
aswshpqfekgasgaaeskptpqstftgpivvdpitrieghlrimvevengkvkdawsss
qlfrgleiilkgrdprdaqhftqracgvctyvhalassrcvddavkvsipanarmmrnlv
masqylhdhlvhfyhlhaldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdk
lkafvesgqlgiftnayflgghkayylppevdliatahylealhmqvkaasamailggkn
phtqftvvggcsnyqgltknplanylalskevcqfvnecyipdllavagfykdwggiggt
snylafgefatddsspekhlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggd
gkhpydgvtdpkytklddkdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdm
vlgklsvpatalhstlgrtaargietaivcanmekwikemadsgakdntlcakwempees
kgvgladaprgalshwirikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiad
pkrpveilrtvhafdpciacgvh

    Sequence, based on observed residues (ATOM records): (download) 
    >4urhR (R:)
kptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprda
qhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlha
ldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayf
lgghkayylppevdliatahylealhmqvkaasamailggknphtqftvvggcsnyqglt
knplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspek
hlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytkldd
kdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgr
taargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwir
ikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpci
acgvh

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >4urhS (S:)
aswshpqfekgasgaaeskptpqstftgpivvdpitrieghlrimvevengkvkdawsss
qlfrgleiilkgrdprdaqhftqracgvctyvhalassrcvddavkvsipanarmmrnlv
masqylhdhlvhfyhlhaldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdk
lkafvesgqlgiftnayflgghkayylppevdliatahylealhmqvkaasamailggkn
phtqftvvggcsnyqgltknplanylalskevcqfvnecyipdllavagfykdwggiggt
snylafgefatddsspekhlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggd
gkhpydgvtdpkytklddkdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdm
vlgklsvpatalhstlgrtaargietaivcanmekwikemadsgakdntlcakwempees
kgvgladaprgalshwirikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiad
pkrpveilrtvhafdpciacgvh

    Sequence, based on observed residues (ATOM records): (download) 
    >4urhS (S:)
kptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprda
qhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhlha
ldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayf
lgghkayylppevdliatahylealhmqvkaasamailggknphtqftvvggcsnyqglt
knplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspek
hlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytkldd
kdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgr
taargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwir
ikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpci
acgvh