PDB entry 1ykm

View 1ykm on RCSB PDB site
Description: Protocatechuate 3,4-Dioxygenase Y408E mutant
Class: oxidoreductase
Keywords: catechol, protocatechuate
Deposited on 2005-01-18, released 2005-08-16
The last revision prior to the SCOP 1.75 freeze date was dated 2006-03-14, with a file datestamp of 2007-06-04.
Experiment type: XRAY
Resolution: 2.22 Å
R-factor: 0.169
AEROSPACI score: 0.51 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: protocatechuate 3,4-dioxygenase alpha chain
    Species: Pseudomonas putida
    Gene: pcaG
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d1ykma1
  • Chain 'B':
    Compound: protocatechuate 3,4-dioxygenase beta chain
    Species: Pseudomonas putida
    Gene: PCAH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00437 (0-237)
      • engineered (107)
      • modified residue (128)
    Domains in SCOP 1.75: d1ykmb1
  • Chain 'C':
    Compound: protocatechuate 3,4-dioxygenase alpha chain
    Species: Pseudomonas putida
    Gene: pcaG
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d1ykmc1
  • Chain 'D':
    Compound: protocatechuate 3,4-dioxygenase beta chain
    Species: Pseudomonas putida
    Gene: PCAH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00437 (0-237)
      • engineered (107)
      • modified residue (128)
    Domains in SCOP 1.75: d1ykmd1
  • Chain 'E':
    Compound: protocatechuate 3,4-dioxygenase alpha chain
    Species: Pseudomonas putida
    Gene: pcaG
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d1ykme1
  • Chain 'F':
    Compound: protocatechuate 3,4-dioxygenase beta chain
    Species: Pseudomonas putida
    Gene: PCAH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00437 (0-237)
      • engineered (107)
      • modified residue (128)
    Domains in SCOP 1.75: d1ykmf1
  • Chain 'G':
    Compound: protocatechuate 3,4-dioxygenase alpha chain
    Species: Pseudomonas putida
    Gene: pcaG
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d1ykmg1
  • Chain 'H':
    Compound: protocatechuate 3,4-dioxygenase beta chain
    Species: Pseudomonas putida
    Gene: PCAH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00437 (0-237)
      • engineered (107)
      • modified residue (128)
    Domains in SCOP 1.75: d1ykmh1
  • Chain 'I':
    Compound: protocatechuate 3,4-dioxygenase alpha chain
    Species: Pseudomonas putida
    Gene: pcaG
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d1ykmi1
  • Chain 'J':
    Compound: protocatechuate 3,4-dioxygenase beta chain
    Species: Pseudomonas putida
    Gene: PCAH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00437 (0-237)
      • engineered (107)
      • modified residue (128)
    Domains in SCOP 1.75: d1ykmj1
  • Chain 'K':
    Compound: protocatechuate 3,4-dioxygenase alpha chain
    Species: Pseudomonas putida
    Gene: pcaG
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d1ykmk1
  • Chain 'L':
    Compound: protocatechuate 3,4-dioxygenase beta chain
    Species: Pseudomonas putida
    Gene: PCAH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00437 (0-237)
      • engineered (107)
      • modified residue (128)
    Domains in SCOP 1.75: d1ykml1
  • Heterogens: FE, HOH

PDB Chain Sequences:

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

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

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

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

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

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

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

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

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

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

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

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