PDB entry 4ko3

View 4ko3 on RCSB PDB site
Description: Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air
Class: oxidoreductase
Keywords: NiFeSe-site, H2 cleavage/production, seleninate, OXIDOREDUCTASE
Deposited on 2013-05-11, released 2013-07-10
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-05-08, with a file datestamp of 2019-05-03.
Experiment type: XRAY
Resolution: 1.7 Å
R-factor: N/A
AEROSPACI score: 0.4 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'L':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: Desulfomicrobium baculatum [TaxId:525897]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C7LN88 (Start-498)
      • conflict (492)
    Domains in SCOPe 2.08: d4ko3l_
  • Chain 'M':
    Compound: Nickel-dependent hydrogenase large subunit
    Species: Desulfomicrobium baculatum [TaxId:525897]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C7LN88 (Start-498)
      • conflict (492)
    Domains in SCOPe 2.08: d4ko3m_
  • Chain 'S':
    Compound: Periplasmic [NiFeSe] hydrogenase small subunit
    Species: Desulfomicrobium baculatum [TaxId:899]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ko3s_
  • Chain 'T':
    Compound: Periplasmic [NiFeSe] hydrogenase small subunit
    Species: Desulfomicrobium baculatum [TaxId:899]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ko3t_
  • Heterogens: SF4, CA, CL, GOL, FCO, NI, H2S, HOH

PDB Chain Sequences:

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >4ko3L (L:)
msqaatpaadgkvkisidpltrveghlkievevkdgkvvdakcsggmfrgfeqilrgrdp
rdssqivqricgvcptahctasvmaqddafgvkvttngritrnlifganylqshilhfyh
laaldyvkgpdvspfvpryanadlltdrikdgakadatntyglnqylkaleirrichemv
amfggrmphvqgmvvggateiptadkvaeyaarfkevqkfvieeylpliytlgsvytdlf
etgigwknviafgvfpedddyktfllkpgvyidgkdeefdsklvkeyvghsffdhsapgg
lhysvgetnpnpdkpgaysfvkaprykdkpcevgplarmwvqnpelspvgqkllkelygi
eaknfrdlgdkafsimgrhvaraeetwltavavekwlkqvqpgaetyvkseipdaaegtg
fteaprgallhylkikdkkienyqivsatlwnanprddmgqrgpieealigvpvpdiknp
vnvgrlvrsydpxlgcavh

    Sequence, based on observed residues (ATOM records): (download) 
    >4ko3L (L:)
gkvkisidpltrveghlkievevkdgkvvdakcsggmfrgfeqilrgrdprdssqivqri
cgvcptahctasvmaqddafgvkvttngritrnlifganylqshilhfyhlaaldyvkgp
dvspfvpryanadlltdrikdgakadatntyglnqylkaleirrichemvamfggrmphv
qgmvvggateiptadkvaeyaarfkevqkfvieeylpliytlgsvytdlfetgigwknvi
afgvfpedddyktfllkpgvyidgkdeefdsklvkeyvghsffdhsapgglhysvgetnp
npdkpgaysfvkaprykdkpcevgplarmwvqnpelspvgqkllkelygieaknfrdlgd
kafsimgrhvaraeetwltavavekwlkqvqpgaetyvkseipdaaegtgfteaprgall
hylkikdkkienyqivsatlwnanprddmgqrgpieealigvpvpdiknpvnvgrlvrsy
dpxlgcavh

  • Chain 'M':
    Sequence, based on SEQRES records: (download) 
    >4ko3M (M:)
msqaatpaadgkvkisidpltrveghlkievevkdgkvvdakcsggmfrgfeqilrgrdp
rdssqivqricgvcptahctasvmaqddafgvkvttngritrnlifganylqshilhfyh
laaldyvkgpdvspfvpryanadlltdrikdgakadatntyglnqylkaleirrichemv
amfggrmphvqgmvvggateiptadkvaeyaarfkevqkfvieeylpliytlgsvytdlf
etgigwknviafgvfpedddyktfllkpgvyidgkdeefdsklvkeyvghsffdhsapgg
lhysvgetnpnpdkpgaysfvkaprykdkpcevgplarmwvqnpelspvgqkllkelygi
eaknfrdlgdkafsimgrhvaraeetwltavavekwlkqvqpgaetyvkseipdaaegtg
fteaprgallhylkikdkkienyqivsatlwnanprddmgqrgpieealigvpvpdiknp
vnvgrlvrsydpxlgcavh

    Sequence, based on observed residues (ATOM records): (download) 
    >4ko3M (M:)
gkvkisidpltrveghlkievevkdgkvvdakcsggmfrgfeqilrgrdprdssqivqri
cgvcptahctasvmaqddafgvkvttngritrnlifganylqshilhfyhlaaldyvkgp
dvspfvpryanadlltdrikdgakadatntyglnqylkaleirrichemvamfggrmphv
qgmvvggateiptadkvaeyaarfkevqkfvieeylpliytlgsvytdlfetgigwknvi
afgvfpedddyktfllkpgvyidgkdeefdsklvkeyvghsffdhsapgglhysvgetnp
npdkpgaysfvkaprykdkpcevgplarmwvqnpelspvgqkllkelygieaknfrdlgd
kafsimgrhvaraeetwltavavekwlkqvqpgaetyvkseipdaaegtgfteaprgall
hylkikdkkienyqivsatlwnanprddmgqrgpieealigvpvpdiknpvnvgrlvrsy
dpxlgcavh

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >4ko3S (S:)
mtegakkapviwvqgqgctgcsvsllnavhprikeilldvislefhptvmasegemalah
myeiaekfngnffllvegaiptakegrycivgetldakghhhevtmmelirdlapkslat
vavgtcsayggipaaegnvtgsksvrdffadekiekllvnvpgcpphpdwmvgtlvaaws
hvlnptehplpeldddgrpllffgdnihencpyldkydnsefaetftkpgckaelgckgp
styadcakrrwnnginwcvenavcigcvepdfpdgkspfyvae

    Sequence, based on observed residues (ATOM records): (download) 
    >4ko3S (S:)
akkapviwvqgqgctgcsvsllnavhprikeilldvislefhptvmasegemalahmyei
aekfngnffllvegaiptakegrycivgetldakghhhevtmmelirdlapkslatvavg
tcsayggipaaegnvtgsksvrdffadekiekllvnvpgcpphpdwmvgtlvaawshvln
ptehplpeldddgrpllffgdnihencpyldkydnsefaetftkpgckaelgckgpstya
dcakrrwnnginwcvenavcigcvepdfpdgkspfyvae

  • Chain 'T':
    Sequence, based on SEQRES records: (download) 
    >4ko3T (T:)
mtegakkapviwvqgqgctgcsvsllnavhprikeilldvislefhptvmasegemalah
myeiaekfngnffllvegaiptakegrycivgetldakghhhevtmmelirdlapkslat
vavgtcsayggipaaegnvtgsksvrdffadekiekllvnvpgcpphpdwmvgtlvaaws
hvlnptehplpeldddgrpllffgdnihencpyldkydnsefaetftkpgckaelgckgp
styadcakrrwnnginwcvenavcigcvepdfpdgkspfyvae

    Sequence, based on observed residues (ATOM records): (download) 
    >4ko3T (T:)
akkapviwvqgqgctgcsvsllnavhprikeilldvislefhptvmasegemalahmyei
aekfngnffllvegaiptakegrycivgetldakghhhevtmmelirdlapkslatvavg
tcsayggipaaegnvtgsksvrdffadekiekllvnvpgcpphpdwmvgtlvaawshvln
ptehplpeldddgrpllffgdnihencpyldkydnsefaetftkpgckaelgckgpstya
dcakrrwnnginwcvenavcigcvepdfpdgkspfyvae