PDB entry 6d0o

View 6d0o on RCSB PDB site
Description: rdpA dioxygenase holoenzyme
Class: oxidoreductase
Keywords: Alpha-ketoglutarate-dependent dioxygenase;, OXIDOREDUCTASE
Deposited on 2018-04-10, released 2018-08-15
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-08-15, with a file datestamp of 2018-08-10.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: N/A
AEROSPACI score: 0.24 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
    Species: Sphingobium herbicidovorans (strain ATCC 700291 / DSM 11019 / NBRC 16415 / MH) [TaxId:1219045]
    Gene: rdpA
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8KSC8 (Start-294)
      • conflict (228-230)
      • conflict (233)
      • conflict (237)
      • conflict (240-241)
      • conflict (245-247)
      • conflict (260)
      • conflict (270)
      • conflict (272-273)
      • conflict (276)
      • conflict (278-279)
      • conflict (281)
      • conflict (283)
      • expression tag (295-299)
    Domains in SCOPe 2.07: d6d0oa1, d6d0oa2
  • Chain 'B':
    Compound: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
    Species: Sphingobium herbicidovorans (strain ATCC 700291 / DSM 11019 / NBRC 16415 / MH) [TaxId:1219045]
    Gene: rdpA
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8KSC8 (Start-294)
      • conflict (228-230)
      • conflict (233)
      • conflict (237)
      • conflict (240-241)
      • conflict (245-247)
      • conflict (260)
      • conflict (270)
      • conflict (272-273)
      • conflict (276)
      • conflict (278-279)
      • conflict (281)
      • conflict (283)
      • expression tag (295-296)
    Domains in SCOPe 2.07: d6d0ob1, d6d0ob2
  • Chain 'C':
    Compound: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
    Species: Sphingobium herbicidovorans (strain ATCC 700291 / DSM 11019 / NBRC 16415 / MH) [TaxId:1219045]
    Gene: rdpA
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8KSC8 (Start-294)
      • conflict (98-99)
      • conflict (228-230)
      • conflict (233)
      • conflict (237)
      • conflict (240-241)
      • conflict (245-247)
      • conflict (260)
      • conflict (270)
      • conflict (272-273)
      • conflict (276)
      • conflict (278-279)
      • conflict (281)
      • conflict (283)
      • expression tag (295-297)
    Domains in SCOPe 2.07: d6d0oc1, d6d0oc2
  • Chain 'D':
    Compound: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
    Species: Sphingobium herbicidovorans (strain ATCC 700291 / DSM 11019 / NBRC 16415 / MH) [TaxId:1219045]
    Gene: rdpA
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8KSC8 (Start-294)
      • conflict (98-99)
      • conflict (228-230)
      • conflict (233)
      • conflict (237)
      • conflict (240-241)
      • conflict (245-247)
      • conflict (260)
      • conflict (270)
      • conflict (272-273)
      • conflict (276)
      • conflict (278-279)
      • conflict (281)
      • conflict (283)
      • expression tag (295-298)
    Domains in SCOPe 2.07: d6d0od1, d6d0od2
  • Heterogens: CO, AKG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6d0oA (A:)
    mhaalsplsqrferiavqpltgvlgaeitgvdlreplddstwneildafhtyqviyfpgq
    aitneqhiafsrrfgpvdpvpllksiegypevqmirregdesgrvigddwhtdstfldap
    paavvmraidvpehggdtgflsmytawetlsptmqatieglnvvhsatrvfgslyqaqnr
    rfsntsvkvmdvdagdretvhplvvthpgsgrkglyvnqvycqriegmsekesepllsfl
    fahatkpeftcrvrwkkdqvvvwdnlctmhyaindyhgqtrilhrttvggvrparhhhhh
    h
    

    Sequence, based on observed residues (ATOM records): (download)
    >6d0oA (A:)
    qrferiavqpltgvlgaeitgvdlreplddstwneildafhtyqviyfpgqaitneqhia
    fsrrfgpvdpvpllksiegypevqmirrigddwhtdstfldappaavvmraidvpehggd
    tgflsmytawetlsptmqatieglnvvhsatrvfgslyqaqnrmdvdagdretvhplvvt
    hpgsgrkglyvnqvycqriegmsekesepllsflfahatkpeftcrvrwkkdqvvvwdnl
    ctmhyaindyhgqtrilhrttvggvrparhhhhh
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6d0oB (B:)
    mhaalsplsqrferiavqpltgvlgaeitgvdlreplddstwneildafhtyqviyfpgq
    aitneqhiafsrrfgpvdpvpllksiegypevqmirregdesgrvigddwhtdstfldap
    paavvmraidvpehggdtgflsmytawetlsptmqatieglnvvhsatrvfgslyqaqnr
    rfsntsvkvmdvdagdretvhplvvthpgsgrkglyvnqvycqriegmsekesepllsfl
    fahatkpeftcrvrwkkdqvvvwdnlctmhyaindyhgqtrilhrttvggvrparhhhhh
    h
    

    Sequence, based on observed residues (ATOM records): (download)
    >6d0oB (B:)
    rferiavqpltgvlgaeitgvdlreplddstwneildafhtyqviyfpgqaitneqhiaf
    srrfgpvdpvpllksiegypevqmirrgddwhtdstfldappaavvmraidvpehggdtg
    flsmytawetlsptmqatieglnvvhsatrvfgslyqaqndvdagdretvhplvvthpgs
    grkglyvnqvycqriegmsekesepllsflfahatkpeftcrvrwkkdqvvvwdnlctmh
    yaindyhgqtrilhrttvggvrparhh
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6d0oC (C:)
    mhaalsplsqrferiavqpltgvlgaeitgvdlreplddstwneildafhtyqviyfpgq
    aitneqhiafsrrfgpvdpvpllksiegypevqmirregdesgrvigddwhtdstfldap
    paavvmraidvpehggdtgflsmytawetlsptmqatieglnvvhsatrvfgslyqaqnr
    rfsntsvkvmdvdagdretvhplvvthpgsgrkglyvnqvycqriegmsekesepllsfl
    fahatkpeftcrvrwkkdqvvvwdnlctmhyaindyhgqtrilhrttvggvrparhhhhh
    h
    

    Sequence, based on observed residues (ATOM records): (download)
    >6d0oC (C:)
    feriavqpltgvlgaeitgvdlreplddstwneildafhtyqviyfpgqaitneqhiafs
    rrfgpvdpvpllksiegypevqmirregdesgrvigddwhtdstfldappaavvmraidv
    pehggdtgflsmytawetlsptmqatieglnvvhsatrvfgslyqaqnrrfsntsvkvmd
    vdagdretvhplvvthpgsgrkglyvnqvycqriegmsekesepllsflfahatkpeftc
    rvrwkkdqvvvwdnlctmhyaindyhgqtrilhrttvggvrparhhh
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6d0oD (D:)
    mhaalsplsqrferiavqpltgvlgaeitgvdlreplddstwneildafhtyqviyfpgq
    aitneqhiafsrrfgpvdpvpllksiegypevqmirregdesgrvigddwhtdstfldap
    paavvmraidvpehggdtgflsmytawetlsptmqatieglnvvhsatrvfgslyqaqnr
    rfsntsvkvmdvdagdretvhplvvthpgsgrkglyvnqvycqriegmsekesepllsfl
    fahatkpeftcrvrwkkdqvvvwdnlctmhyaindyhgqtrilhrttvggvrparhhhhh
    h
    

    Sequence, based on observed residues (ATOM records): (download)
    >6d0oD (D:)
    rferiavqpltgvlgaeitgvdlreplddstwneildafhtyqviyfpgqaitneqhiaf
    srrfgpvdpvpllksiegypevqmirregdesgrvigddwhtdstfldappaavvmraid
    vpehggdtgflsmytawetlsptmqatieglnvvhsatrvfgslyqaqnrrfsntsvkvm
    dvdagdretvhplvvthpgsgrkglyvnqvycqriegmsekesepllsflfahatkpeft
    crvrwkkdqvvvwdnlctmhyaindyhgqtrilhrttvggvrparhhhh