PDB entry 4uql

View 4uql on RCSB PDB site
Description: High-resolution structure of a Ni-A Ni-Sox mixture of the D. fructosovorans NiFe-hydrogenase L122A mutant
Class: oxidoreductase
Keywords: oxidoreductase, nife-site, ni-a state, sulfenate, ni-sox state, persulfide
Deposited on 2014-06-24, released 2014-10-29
The last revision prior to the SCOPe 2.07 freeze date was dated 2015-01-21, with a file datestamp of 2015-01-16.
Experiment type: XRAY
Resolution: 1.22 Å
R-factor: 0.12202
AEROSPACI score: 0.76 (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 2.07: d4uqla_
  • Chain 'B':
    Compound: Hydrogenase (NiFe) small subunit HydA
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d4uqlb_
  • Chain 'Q':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed):
    • Uniprot E1K247 (Start-562)
      • engineered mutation (135)
    Domains in SCOPe 2.07: d4uqlq_
  • Chain 'R':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: Desulfovibrio fructosovorans [TaxId:878]
    Database cross-references and differences (RAF-indexed):
    • Uniprot E1K247 (Start-562)
      • engineered mutation (135)
    Domains in SCOPe 2.07: d4uqlr_
  • Heterogens: SF4, F3S, GOL, GLY, SOT, H2S, FCO, NI, MG, CL, HOH

PDB Chain Sequences:

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

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

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

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

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

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

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

    Sequence, based on observed residues (ATOM records): (download) 
    >4uqlR (R:)
kptpqstftgpivvdpitrieghlrimvevengkvkdawsssqlfrgleiilkgrdprda
qhftqracgvctyvhalassrcvddavkvsipanarmmrnlvmasqylhdhlvhfyhaha
ldwvdvtaalkadpnkaaklaasiaparpgnsakalkavqdklkafvesgqlgiftnayf
lgghkayylppevdliatahylealhmqvkaasamailggknphtqftvvggcsnyqglt
kdplanylalskevcqfvnecyipdllavagfykdwggiggtsnylafgefatddsspek
hlatsqfpsgvitgrdlgkvdnvdlgaiyedvkyswyapggdgkhpydgvtdpkytkldd
kdhyswmkaprykgkamevgplartfiayakgqpdfkkvvdmvlgklsvpatalhstlgr
taargietaivcanmekwikemadsgakdntlcakwempeeskgvgladaprgalshwir
ikgkkidnfqlvvpstwnlgprgaqgdkspveealigtpiadpkrpveilrtvhafdpci
acgvh