PDB entry 5mdl

View 5mdl on RCSB PDB site
Description: Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its O2-derivatized form by a "soak-and-freeze" derivatization method
Class: oxidoreductase
Keywords: [NIFE] HYDROGENASE, KNALLGASBACTERIA, PROTEOBACTERIA, AEROBIC HYDROGEN BACTERIA, OXYGEN DERIVATISATION, 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, OXYGEN DERIVATISED STATE, OXIDIZED STATE, 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: 1.41 Å
R-factor: N/A
AEROSPACI score: 0.53 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'L':
    Compound: Uptake hydrogenase large subunit;HOXG
    Species: Ralstonia eutropha [TaxId:381666]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5mdll_
  • Chain 'S':
    Compound: Uptake hydrogenase small subunit;HOXK
    Species: Ralstonia eutropha [TaxId:381666]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5mdls_
  • Heterogens: NFV, MG, OXY, PEG, SF4, F3S, F4S, CL, O, HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download) 
    >5mdlL (L:)
ayatqgfnlddrgrrivvdpvtrieghmrcevnvdannvirnavstgtmwrglevilkgr
dprdawafvericgvctgchalasvravenaldiripknahlireimaktlqvhdhavhf
yhlhaldwvdvmsalkadpkrtselqqlvspahplssagyfrdiqnrlkrfvesgqlgpf
mngywgskayvlppeanlmavthylealdlqkewvkihtifggknphpnylvggvpcain
ldggaasapvnmerlsfvkarideiiefnknvyvpdvlaigtlykqagwlyggglaatnv
ldygeypnvaynkstdqlpggailngnwdevfpvdprdsqqvqefvshswykyadesvgl
hpwdgvtepnyvlgantkgtrtrieqidesakyswiksprwrghamevgplsryilayah
arsgnkyaerpkeqleysaqminsaipkalglpetqytlkqllpstigrtlaralesqyc
gemmhsdwhdlvaniragdtatanvdkwdpatwplqakgvgtvaaprgalghwirikdgr
ienyqcvvpttwngsprdykgqigafeaslmntpmvnpeqpveilrtlhsfdpclacsth

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

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