PDB entry 1ykp

View 1ykp on RCSB PDB site
Description: Protocatechuate 3,4-Dioxygenase Y408H mutant bound to DHB
Class: oxidoreductase
Keywords: protocatechuate, catechol, OXIDOREDUCTASE
Deposited on 2005-01-18, released 2005-08-16
The last revision prior to the SCOPe 2.07 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 2.41 Å
R-factor: 0.145
AEROSPACI score: 0.37 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: protocatechuate 3,4-dioxygenase alpha chain
    Species: Pseudomonas putida [TaxId:303]
    Gene: pcaG
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1ykpa_
  • Chain 'B':
    Compound: protocatechuate 3,4-dioxygenase beta chain
    Species: Pseudomonas putida [TaxId:303]
    Gene: PCAH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00437 (0-237)
      • engineered (107)
      • modified residue (128)
    Domains in SCOPe 2.07: d1ykpb_
  • Chain 'C':
    Compound: protocatechuate 3,4-dioxygenase alpha chain
    Species: Pseudomonas putida [TaxId:303]
    Gene: pcaG
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1ykpc_
  • Chain 'D':
    Compound: protocatechuate 3,4-dioxygenase beta chain
    Species: Pseudomonas putida [TaxId:303]
    Gene: PCAH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00437 (0-237)
      • engineered (107)
      • modified residue (128)
    Domains in SCOPe 2.07: d1ykpd_
  • Chain 'E':
    Compound: protocatechuate 3,4-dioxygenase alpha chain
    Species: Pseudomonas putida [TaxId:303]
    Gene: pcaG
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1ykpe_
  • Chain 'F':
    Compound: protocatechuate 3,4-dioxygenase beta chain
    Species: Pseudomonas putida [TaxId:303]
    Gene: PCAH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00437 (0-237)
      • engineered (107)
      • modified residue (128)
    Domains in SCOPe 2.07: d1ykpf_
  • Chain 'G':
    Compound: protocatechuate 3,4-dioxygenase alpha chain
    Species: Pseudomonas putida [TaxId:303]
    Gene: pcaG
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1ykpg_
  • Chain 'H':
    Compound: protocatechuate 3,4-dioxygenase beta chain
    Species: Pseudomonas putida [TaxId:303]
    Gene: PCAH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00437 (0-237)
      • engineered (107)
      • modified residue (128)
    Domains in SCOPe 2.07: d1ykph_
  • Chain 'I':
    Compound: protocatechuate 3,4-dioxygenase alpha chain
    Species: Pseudomonas putida [TaxId:303]
    Gene: pcaG
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1ykpi_
  • Chain 'J':
    Compound: protocatechuate 3,4-dioxygenase beta chain
    Species: Pseudomonas putida [TaxId:303]
    Gene: PCAH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00437 (0-237)
      • engineered (107)
      • modified residue (128)
    Domains in SCOPe 2.07: d1ykpj_
  • Chain 'K':
    Compound: protocatechuate 3,4-dioxygenase alpha chain
    Species: Pseudomonas putida [TaxId:303]
    Gene: pcaG
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1ykpk_
  • Chain 'L':
    Compound: protocatechuate 3,4-dioxygenase beta chain
    Species: Pseudomonas putida [TaxId:303]
    Gene: PCAH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00437 (0-237)
      • engineered (107)
      • modified residue (128)
    Domains in SCOPe 2.07: d1ykpl_
  • Heterogens: FE, DHB, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1ykpA (A:)
    piellpetpsqtagpyvhiglaleaagnptrdqeiwnrlakpdapgehilllgqvydgng
    hlvrdsflevwqadangeyqdaynlenafnsfgrtattfdagewtlhtvkpgvvnnaagv
    pmaphinislfarginihlhtrlyfddeaqanakcpvlnlieqpqrretliakrcevdgk
    tayrfdiriqgegetvffdf
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1ykpB (B:)
    paqdnsrfvirdrnwhpkaltpdyktsiarsprqalvsipqsisettgpnfshlgfgahd
    hdlllnfnngglpigeriivagrvvdqygkpvpntlvemwqanaggrhrhkndrylapld
    pnfggvgrcltdsdgyysfrtikpgpypwrngpndwrpahihfgisgpsiatklitqlyf
    egdplipmcpivksianpeavqqliakldmnnanpmdclayrfdivlrgqrkthfenc
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1ykpC (C:)
    piellpetpsqtagpyvhiglaleaagnptrdqeiwnrlakpdapgehilllgqvydgng
    hlvrdsflevwqadangeyqdaynlenafnsfgrtattfdagewtlhtvkpgvvnnaagv
    pmaphinislfarginihlhtrlyfddeaqanakcpvlnlieqpqrretliakrcevdgk
    tayrfdiriqgegetvffdf
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1ykpD (D:)
    paqdnsrfvirdrnwhpkaltpdyktsiarsprqalvsipqsisettgpnfshlgfgahd
    hdlllnfnngglpigeriivagrvvdqygkpvpntlvemwqanaggrhrhkndrylapld
    pnfggvgrcltdsdgyysfrtikpgpypwrngpndwrpahihfgisgpsiatklitqlyf
    egdplipmcpivksianpeavqqliakldmnnanpmdclayrfdivlrgqrkthfenc
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1ykpE (E:)
    piellpetpsqtagpyvhiglaleaagnptrdqeiwnrlakpdapgehilllgqvydgng
    hlvrdsflevwqadangeyqdaynlenafnsfgrtattfdagewtlhtvkpgvvnnaagv
    pmaphinislfarginihlhtrlyfddeaqanakcpvlnlieqpqrretliakrcevdgk
    tayrfdiriqgegetvffdf
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1ykpF (F:)
    paqdnsrfvirdrnwhpkaltpdyktsiarsprqalvsipqsisettgpnfshlgfgahd
    hdlllnfnngglpigeriivagrvvdqygkpvpntlvemwqanaggrhrhkndrylapld
    pnfggvgrcltdsdgyysfrtikpgpypwrngpndwrpahihfgisgpsiatklitqlyf
    egdplipmcpivksianpeavqqliakldmnnanpmdclayrfdivlrgqrkthfenc
    

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1ykpG (G:)
    piellpetpsqtagpyvhiglaleaagnptrdqeiwnrlakpdapgehilllgqvydgng
    hlvrdsflevwqadangeyqdaynlenafnsfgrtattfdagewtlhtvkpgvvnnaagv
    pmaphinislfarginihlhtrlyfddeaqanakcpvlnlieqpqrretliakrcevdgk
    tayrfdiriqgegetvffdf
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1ykpH (H:)
    paqdnsrfvirdrnwhpkaltpdyktsiarsprqalvsipqsisettgpnfshlgfgahd
    hdlllnfnngglpigeriivagrvvdqygkpvpntlvemwqanaggrhrhkndrylapld
    pnfggvgrcltdsdgyysfrtikpgpypwrngpndwrpahihfgisgpsiatklitqlyf
    egdplipmcpivksianpeavqqliakldmnnanpmdclayrfdivlrgqrkthfenc
    

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1ykpI (I:)
    piellpetpsqtagpyvhiglaleaagnptrdqeiwnrlakpdapgehilllgqvydgng
    hlvrdsflevwqadangeyqdaynlenafnsfgrtattfdagewtlhtvkpgvvnnaagv
    pmaphinislfarginihlhtrlyfddeaqanakcpvlnlieqpqrretliakrcevdgk
    tayrfdiriqgegetvffdf
    

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1ykpJ (J:)
    paqdnsrfvirdrnwhpkaltpdyktsiarsprqalvsipqsisettgpnfshlgfgahd
    hdlllnfnngglpigeriivagrvvdqygkpvpntlvemwqanaggrhrhkndrylapld
    pnfggvgrcltdsdgyysfrtikpgpypwrngpndwrpahihfgisgpsiatklitqlyf
    egdplipmcpivksianpeavqqliakldmnnanpmdclayrfdivlrgqrkthfenc
    

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1ykpK (K:)
    piellpetpsqtagpyvhiglaleaagnptrdqeiwnrlakpdapgehilllgqvydgng
    hlvrdsflevwqadangeyqdaynlenafnsfgrtattfdagewtlhtvkpgvvnnaagv
    pmaphinislfarginihlhtrlyfddeaqanakcpvlnlieqpqrretliakrcevdgk
    tayrfdiriqgegetvffdf
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1ykpL (L:)
    paqdnsrfvirdrnwhpkaltpdyktsiarsprqalvsipqsisettgpnfshlgfgahd
    hdlllnfnngglpigeriivagrvvdqygkpvpntlvemwqanaggrhrhkndrylapld
    pnfggvgrcltdsdgyysfrtikpgpypwrngpndwrpahihfgisgpsiatklitqlyf
    egdplipmcpivksianpeavqqliakldmnnanpmdclayrfdivlrgqrkthfenc