PDB entry 3gdk

View 3gdk on RCSB PDB site
Description: Crystal structure of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae
Class: lyase
Keywords: orotidine 5'-monophosphate decarboxylase, Saccharomyces cerevisiae, crystal structure, Decarboxylase, Lyase, Phosphoprotein, Pyrimidine biosynthesis, Ubl conjugation
Deposited on 2009-02-24, released 2009-06-23
The last revision prior to the SCOPe 2.01 freeze date was dated 2009-06-23, with a file datestamp of 2009-06-19.
Experiment type: XRAY
Resolution: 2 Å
R-factor: 0.249
AEROSPACI score: 0.39 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: orotidine 5'-phosphate decarboxylase
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: URA3, YEL021W
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3gdka_
  • Chain 'B':
    Compound: orotidine 5'-phosphate decarboxylase
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: URA3, YEL021W
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3gdkb_
  • Chain 'C':
    Compound: orotidine 5'-phosphate decarboxylase
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: URA3, YEL021W
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3gdkc_
  • Chain 'D':
    Compound: orotidine 5'-phosphate decarboxylase
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: URA3, YEL021W
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3gdkd_
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3gdkA (A:)
    mskatykeraathpspvaaklfnimhekqtnlcasldvrttkellelvealgpkicllkt
    hvdiltdfsmegtvkplkalsakynfllfedrkfadigntvklqysagvyriaewaditn
    ahgvvgpgivsglkqaaeevtkeprgllmlaelsckgslatgeytkgtvdiaksdkdfvi
    gfiaqrdmggrdegydwlimtpgvglddkgdalgqqyrtvddvvstgsdiiivgrglfak
    grdakvegeryrkagweaylrrcgqqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3gdkA (A:)
    katykeraathpspvaaklfnimhekqtnlcasldvrttkellelvealgpkicllkthv
    diltdfsmegtvkplkalsakynfllfedrkfadigntvklqysagvyriaewaditnah
    gvvgpgivsglkqaaeevtkeprgllmlaelsckgslatgeytkgtvdiaksdkdfvigf
    iaqrdmggrdegydwlimtpgvglddkgdalgqqyrtvddvvstgsdiiivgrglfakgr
    dakvegeryrkagweaylrr
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3gdkB (B:)
    mskatykeraathpspvaaklfnimhekqtnlcasldvrttkellelvealgpkicllkt
    hvdiltdfsmegtvkplkalsakynfllfedrkfadigntvklqysagvyriaewaditn
    ahgvvgpgivsglkqaaeevtkeprgllmlaelsckgslatgeytkgtvdiaksdkdfvi
    gfiaqrdmggrdegydwlimtpgvglddkgdalgqqyrtvddvvstgsdiiivgrglfak
    grdakvegeryrkagweaylrrcgqqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3gdkB (B:)
    katykeraathpspvaaklfnimhekqtnlcasldvrttkellelvealgpkicllkthv
    diltdfsmegtvkplkalsakynfllfedrkfadigntvklqysagvyriaewaditnah
    gvvgpgivsglkqaaeevtkeprgllmlaelsckgslatgeytkgtvdiaksdkdfvigf
    iaqrdmggrdegydwlimtpgvglddkgdalgqqyrtvddvvstgsdiiivgrglfakgr
    dakvegeryrkagweaylrr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3gdkC (C:)
    mskatykeraathpspvaaklfnimhekqtnlcasldvrttkellelvealgpkicllkt
    hvdiltdfsmegtvkplkalsakynfllfedrkfadigntvklqysagvyriaewaditn
    ahgvvgpgivsglkqaaeevtkeprgllmlaelsckgslatgeytkgtvdiaksdkdfvi
    gfiaqrdmggrdegydwlimtpgvglddkgdalgqqyrtvddvvstgsdiiivgrglfak
    grdakvegeryrkagweaylrrcgqqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3gdkC (C:)
    katykeraathpspvaaklfnimhekqtnlcasldvrttkellelvealgpkicllkthv
    diltdfsmegtvkplkalsakynfllfedrkfadigntvklqysagvyriaewaditnah
    gvvgpgivsglkqaaeevtkeprgllmlaelsckgslatgeytkgtvdiaksdkdfvigf
    iaqrdmggrdegydwlimtpgvgrtvddvvstgsdiiivgrglfakgrdakvegeryrka
    gweaylrrcgqq
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3gdkD (D:)
    mskatykeraathpspvaaklfnimhekqtnlcasldvrttkellelvealgpkicllkt
    hvdiltdfsmegtvkplkalsakynfllfedrkfadigntvklqysagvyriaewaditn
    ahgvvgpgivsglkqaaeevtkeprgllmlaelsckgslatgeytkgtvdiaksdkdfvi
    gfiaqrdmggrdegydwlimtpgvglddkgdalgqqyrtvddvvstgsdiiivgrglfak
    grdakvegeryrkagweaylrrcgqqn
    

    Sequence, based on observed residues (ATOM records): (download)
    >3gdkD (D:)
    katykeraathpspvaaklfnimhekqtnlcasldvrttkellelvealgpkicllkthv
    diltdfsmegtvkplkalsakynfllfedrkfadigntvklqysagvyriaewaditnah
    gvvgpgivsglkqaaeevtkeprgllmlaelsckgslatgeytkgtvdiaksdkdfvigf
    iaqrdmggrdegydwlimtpgvgrtvddvvstgsdiiivgrglfakgrdakvegeryrka
    gweaylrrcgqq