PDB entry 5mdk

View 5mdk on RCSB PDB site
Description: Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form (oxidized state - state 3)
Class: oxidoreductase
Keywords: [NIFE] HYDROGENASE, KNALLGASBACTERIA, PROTEOBACTERIA, AEROBIC HYDROGEN BACTERIA, DEHYDROGENASE, OXIDOREDUCTASE, HYDROGEN CATALYSIS, METALLOENZYME, DIHYDROGEN, BIMETALLIC, METALLOPROTEIN CATALYTIC CENTER, NI-FE ACTIVE SITE, T-CLUSTER, FE-S CLUSTER, [4Fe-3S] CLUSTER, [3Fe-4S] CLUSTER, [4Fe-4S] CLUSTER, AS-ISOLATED STATE, OXIDIZED STATE, NATIVE, OXYGEN TOLERANT HYDROGENASE, MEMBRANE BOUND, MEMBRANE, HYDROPHOBIC TUNNEL, GAS TRANSPORT
Deposited on 2016-11-11, released 2018-02-21
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-01-30, with a file datestamp of 2019-01-25.
Experiment type: XRAY
Resolution: 1.5 Å
R-factor: N/A
AEROSPACI score: 0.48 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'L':
    Compound: Uptake hydrogenase large subunit; HOXG
    Species: Ralstonia eutropha H16 [TaxId:381666]
    Gene: HOXG
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5mdkl_
  • Chain 'S':
    Compound: Uptake hydrogenase small subunit; HOXK
    Species: Ralstonia eutropha H16 [TaxId:381666]
    Gene: HOXK
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5mdks_
  • Heterogens: MG, CL, NFV, SF4, F3S, F4S, HOH

PDB Chain Sequences:

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >5mdkL (L:)
msayatqgfnlddrgrrivvdpvtrieghmrcevnvdannvirnavstgtmwrglevilk
grdprdawafvericgvctgchalasvravenaldiripknahlireimaktlqvhdhav
hfyhlhaldwvdvmsalkadpkrtselqqlvspahplssagyfrdiqnrlkrfvesgqlg
pfmngywgskayvlppeanlmavthylealdlqkewvkihtifggknphpnylvggvpca
inldgigaasapvnmerlsfvkarideiiefnknvyvpdvlaigtlykqagwlyggglaa
tnvldygeypnvaynkstdqlpggailngnwdevfpvdprdsqqvqefvshswykyades
vglhpwdgvtepnyvlgantkgtrtrieqidesakyswiksprwrghamevgplsryila
yaharsgnkyaerpkeqleysaqminsaipkalglpetqytlkqllpstigrtlarales
qycgemmhsdwhdlvaniragdtatanvdkwdpatwplqakgvgtvaaprgalghwirik
dgrienyqcvvpttwngsprdykgqigafeaslmntpmvnpeqpveilrtlhsfdpclac
sth

    Sequence, based on observed residues (ATOM records): (download) 
    >5mdkL (L:)
ayatqgfnlddrgrrivvdpvtrieghmrcevnvdannvirnavstgtmwrglevilkgr
dprdawafvericgvctgchalasvravenaldiripknahlireimaktlqvhdhavhf
yhlhaldwvdvmsalkadpkrtselqqlvspahplssagyfrdiqnrlkrfvesgqlgpf
mngywgskayvlppeanlmavthylealdlqkewvkihtifggknphpnylvggvpcain
ldgaasapvnmerlsfvkarideiiefnknvyvpdvlaigtlykqagwlyggglaatnvl
dygeypnvaynkstdqlpggailngnwdevfpvdprdsqqvqefvshswykyadesvglh
pwdgvtepnyvlgantkgtrtrieqidesakyswiksprwrghamevgplsryilayaha
rsgnkyaerpkeqleysaqminsaipkalglpetqytlkqllpstigrtlaralesqycg
emmhsdwhdlvaniragdtatanvdkwdpatwplqakgvgtvaaprgalghwirikdgri
enyqcvvpttwngsprdykgqigafeaslmntpmvnpeqpveilrtlhsfdpclacsth

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >5mdkS (S:)
metkprtpvlwlhglectccsesfirsahplakdvvlsmisldyddtlmaaaghqaeail
eeimtkykgnyilavegnpplnqdgmsciiggrpfieqlkyvakdakaiiswgscaswgc
vqaakpnptqatpvhkvitdkpiikvpgcppiaevmtgvitymltfdripeldrqgrpkm
fysqrihdkcyrrphfdagqfveewddesarkgfclykmgckgpttynacsttrwnegts
fpiqsghgcigcsedgfwdkgsfydrltgisqfgveanadkiggtasvvvgaavtahaaa
saikraskknetsgsehrsawshpqfek

    Sequence, based on observed residues (ATOM records): (download) 
    >5mdkS (S:)
prtpvlwlhglectccsesfirsahplakdvvlsmisldyddtlmaaaghqaeaileeim
tkykgnyilavegnpplnqdgmsciiggrpfieqlkyvakdakaiiswgscaswgcvqaa
kpnptqatpvhkvitdkpiikvpgcppiaevmtgvitymltfdripeldrqgrpkmfysq
rihdkcyrrphfdagqfveewddesarkgfclykmgckgpttynacsttrwnegtsfpiq
sghgcigcsedgfwdkgsfydrltgisqf