PDB entry 3ek5

View 3ek5 on RCSB PDB site
Description: Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen Bacterium
Class: transferase
Keywords: Xanthomonas campestris, UMPK crystal structure, unique GTP binding site, allosteric regulation, ATP-binding, Kinase, Nucleotide-binding, Pyrimidine biosynthesis, Transferase
Deposited on 2008-09-18, released 2008-12-23
The last revision prior to the SCOPe 2.08 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 2.56 Å
R-factor: 0.209
AEROSPACI score: 0.29 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: uridylate kinase
    Species: Xanthomonas campestris pv. campestris [TaxId:340]
    Gene: pyrH, XCC1371
    Database cross-references and differences (RAF-indexed):
    • Uniprot P59009 (3-242)
      • expression tag (1-2)
    Domains in SCOPe 2.08: d3ek5a1, d3ek5a2
  • Chain 'B':
    Compound: uridylate kinase
    Species: Xanthomonas campestris pv. campestris [TaxId:340]
    Gene: pyrH, XCC1371
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3ek5b_
  • Chain 'C':
    Compound: uridylate kinase
    Species: Xanthomonas campestris pv. campestris [TaxId:340]
    Gene: pyrH, XCC1371
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3ek5c_
  • Chain 'D':
    Compound: uridylate kinase
    Species: Xanthomonas campestris pv. campestris [TaxId:340]
    Gene: pyrH, XCC1371
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3ek5d_
  • Chain 'E':
    Compound: uridylate kinase
    Species: Xanthomonas campestris pv. campestris [TaxId:340]
    Gene: pyrH, XCC1371
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3ek5e_
  • Chain 'F':
    Compound: uridylate kinase
    Species: Xanthomonas campestris pv. campestris [TaxId:340]
    Gene: pyrH, XCC1371
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3ek5f_
  • Heterogens: GTP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3ek5A (A:)
snamselsyrrillklsgealmgdgdygidpkvinrlahevieaqqagaqvalvigggni
frgaglaasgmdrvtgdhmgmlatvinalamqdaleklgakvrvmsaikindvcedfirr
rairhlekgriaifaagtgnpffttdsgaalraieigadlllkatkvdgvydkdpkkhsd
avrydsltydevimqglevmdtaafalardsdlplrifgmsepgvllrilhgaqigtlvq
grs

    Sequence, based on observed residues (ATOM records): (download) 
    >3ek5A (A:)
namselsyrrillklsgealmgdgdygidpkvinrlahevieaqqagaqvalvigggnif
rgaglaasgmdrvtgdhmgmlatvinalamqdaleklgakvrvmsaikindvcedfirrr
airhlekgriaifaagtgnpffttdsgaalraieigadlllkatkvdgvydkdpkkhsda
vrydsltydevimqglevmdtaafalardsdlplrifgmsepgvllrilhgaqigtlvqg
rs

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3ek5B (B:)
snamselsyrrillklsgealmgdgdygidpkvinrlahevieaqqagaqvalvigggni
frgaglaasgmdrvtgdhmgmlatvinalamqdaleklgakvrvmsaikindvcedfirr
rairhlekgriaifaagtgnpffttdsgaalraieigadlllkatkvdgvydkdpkkhsd
avrydsltydevimqglevmdtaafalardsdlplrifgmsepgvllrilhgaqigtlvq
grs

    Sequence, based on observed residues (ATOM records): (download) 
    >3ek5B (B:)
selsyrrillklsgealmgdgdygidpkvinrlahevieaqqagaqvalvigggnifrga
glaasgmdrvtgdhmgmlatvinalamqdaleklgakvrvmsaikindvcedfirrrair
hlekgriaifaagtgnpffttdsgaalraieigadlllkatkvdgvydkdpkkhsdavry
dsltydevimqglevmdtaafalardsdlplrifgmsepgvllrilhgaqigtlvqgrs

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >3ek5C (C:)
snamselsyrrillklsgealmgdgdygidpkvinrlahevieaqqagaqvalvigggni
frgaglaasgmdrvtgdhmgmlatvinalamqdaleklgakvrvmsaikindvcedfirr
rairhlekgriaifaagtgnpffttdsgaalraieigadlllkatkvdgvydkdpkkhsd
avrydsltydevimqglevmdtaafalardsdlplrifgmsepgvllrilhgaqigtlvq
grs

    Sequence, based on observed residues (ATOM records): (download) 
    >3ek5C (C:)
selsyrrillklsgealmgdgdygidpkvinrlahevieaqqagaqvalvigggnifrga
glaasgmdrvtgdhmgmlatvinalamqdaleklgakvrvmsaikindvcedfirrrair
hlekgriaifaagtgnpffttdsgaalraieigadlllkatkvdgvydkdpkkhsdavry
dsltydevimqglevmdtaafalardsdlplrifgmsepgvllrilhgaqigtlvqgrs

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3ek5D (D:)
snamselsyrrillklsgealmgdgdygidpkvinrlahevieaqqagaqvalvigggni
frgaglaasgmdrvtgdhmgmlatvinalamqdaleklgakvrvmsaikindvcedfirr
rairhlekgriaifaagtgnpffttdsgaalraieigadlllkatkvdgvydkdpkkhsd
avrydsltydevimqglevmdtaafalardsdlplrifgmsepgvllrilhgaqigtlvq
grs

    Sequence, based on observed residues (ATOM records): (download) 
    >3ek5D (D:)
selsyrrillklsgealmgdgdygidpkvinrlahevieaqqagaqvalvigggnifrga
glaasgmdrvtgdhmgmlatvinalamqdaleklgakvrvmsaikindvcedfirrrair
hlekgriaifaagtgnpffttdsgaalraieigadlllkatkvdgvydkdpkkhsdavry
dsltydevimqglevmdtaafalardsdlplrifgmsepgvllrilhgaqigtlvqgrs

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >3ek5E (E:)
snamselsyrrillklsgealmgdgdygidpkvinrlahevieaqqagaqvalvigggni
frgaglaasgmdrvtgdhmgmlatvinalamqdaleklgakvrvmsaikindvcedfirr
rairhlekgriaifaagtgnpffttdsgaalraieigadlllkatkvdgvydkdpkkhsd
avrydsltydevimqglevmdtaafalardsdlplrifgmsepgvllrilhgaqigtlvq
grs

    Sequence, based on observed residues (ATOM records): (download) 
    >3ek5E (E:)
selsyrrillklsgealmgdgdygidpkvinrlahevieaqqagaqvalvigggnifrga
glaasgmdrvtgdhmgmlatvinalamqdaleklgakvrvmsaikindvcedfirrrair
hlekgriaifaagtgnpffttdsgaalraieigadlllkatkvdgvydkdpkkhsdavry
dsltydevimqglevmdtaafalardsdlplrifgmsepgvllrilhgaqigtlvqgrs

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >3ek5F (F:)
snamselsyrrillklsgealmgdgdygidpkvinrlahevieaqqagaqvalvigggni
frgaglaasgmdrvtgdhmgmlatvinalamqdaleklgakvrvmsaikindvcedfirr
rairhlekgriaifaagtgnpffttdsgaalraieigadlllkatkvdgvydkdpkkhsd
avrydsltydevimqglevmdtaafalardsdlplrifgmsepgvllrilhgaqigtlvq
grs

    Sequence, based on observed residues (ATOM records): (download) 
    >3ek5F (F:)
selsyrrillklsgealmgdgdygidpkvinrlahevieaqqagaqvalvigggnifrga
glaasgmdrvtgdhmgmlatvinalamqdaleklgakvrvmsaikindvcedfirrrair
hlekgriaifaagtgnpffttdsgaalraieigadlllkatkvdgvydkdpkkhsdavry
dsltydevimqglevmdtaafalardsdlplrifgmsepgvllrilhgaqigtlvqgrs