PDB entry 3gdt

View 3gdt on RCSB PDB site
Description: Crystal structure of the D91N mutant of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae complexed with 6-azauridine 5'-monophosphate
Class: lyase
Keywords: orotidine 5'-monophosphate decarboxylase, D91N mutant, 6-azauridine 5'-monophosphate, 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 2.07 freeze date was dated 2009-06-23, with a file datestamp of 2009-06-19.
Experiment type: XRAY
Resolution: 1.6 Å
R-factor: 0.236
AEROSPACI score: 0.53 (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):
    • Uniprot P03962
      • engineered (90)
    Domains in SCOPe 2.07: d3gdta_
  • Chain 'B':
    Compound: orotidine 5'-phosphate decarboxylase
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: URA3, YEL021W
    Database cross-references and differences (RAF-indexed):
    • Uniprot P03962
      • engineered (90)
    Domains in SCOPe 2.07: d3gdtb_
  • Chain 'C':
    Compound: orotidine 5'-phosphate decarboxylase
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: URA3, YEL021W
    Database cross-references and differences (RAF-indexed):
    • Uniprot P03962
      • engineered (90)
    Domains in SCOPe 2.07: d3gdtc_
  • Chain 'D':
    Compound: orotidine 5'-phosphate decarboxylase
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Gene: URA3, YEL021W
    Database cross-references and differences (RAF-indexed):
    • Uniprot P03962
      • engineered (90)
    Domains in SCOPe 2.07: d3gdtd_
  • Heterogens: UP6, HOH

PDB Chain Sequences:

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

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

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

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

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

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

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

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