PDB entry 6ybh

View 6ybh on RCSB PDB site
Description: Deoxyribonucleoside Kinase
Class: transferase
Keywords: Transferase
Deposited on 2020-03-17, released 2021-03-31
The last revision prior to the SCOPe 2.07 freeze date was dated 2021-03-31, with a file datestamp of 2021-03-26.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: N/A
AEROSPACI score: 0.29 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: deoxynucleoside kinase
    Species: Drosophila melanogaster [TaxId:7227]
    Gene: dnk, CG5452
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9XZT6 (1-End)
      • initiating methionine (0)
      • engineered mutation (7)
      • engineered mutation (11)
      • engineered mutation (33)
      • engineered mutation (69)
      • engineered mutation (79)
      • engineered mutation (82)
      • engineered mutation (88)
      • engineered mutation (111)
      • engineered mutation (133)
      • engineered mutation (154)
      • engineered mutation (156)
      • engineered mutation (158)
      • engineered mutation (161-162)
      • engineered mutation (166)
      • engineered mutation (170)
      • engineered mutation (173)
  • Chain 'B':
    Compound: deoxynucleoside kinase
    Species: Drosophila melanogaster [TaxId:7227]
    Gene: dnk, CG5452
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9XZT6 (1-End)
      • initiating methionine (0)
      • engineered mutation (7)
      • engineered mutation (11)
      • engineered mutation (33)
      • engineered mutation (69)
      • engineered mutation (79)
      • engineered mutation (82)
      • engineered mutation (88)
      • engineered mutation (111)
      • engineered mutation (133)
      • engineered mutation (154)
      • engineered mutation (156)
      • engineered mutation (158)
      • engineered mutation (161-162)
      • engineered mutation (166)
      • engineered mutation (170)
      • engineered mutation (173)
    Domains in SCOPe 2.07: d6ybhb_
  • Chain 'C':
    Compound: deoxynucleoside kinase
    Species: Drosophila melanogaster [TaxId:7227]
    Gene: dnk, CG5452
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9XZT6 (1-End)
      • initiating methionine (0)
      • engineered mutation (7)
      • engineered mutation (11)
      • engineered mutation (33)
      • engineered mutation (69)
      • engineered mutation (79)
      • engineered mutation (82)
      • engineered mutation (88)
      • engineered mutation (111)
      • engineered mutation (133)
      • engineered mutation (154)
      • engineered mutation (162)
      • engineered mutation (166)
      • engineered mutation (170)
      • engineered mutation (173)
  • Chain 'D':
    Compound: deoxynucleoside kinase
    Species: Drosophila melanogaster [TaxId:7227]
    Gene: dnk, CG5452
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9XZT6 (1-End)
      • initiating methionine (0)
      • engineered mutation (7)
      • engineered mutation (11)
      • engineered mutation (33)
      • engineered mutation (69)
      • engineered mutation (79)
      • engineered mutation (82)
      • engineered mutation (88)
      • engineered mutation (111)
      • engineered mutation (133)
      • engineered mutation (154)
      • engineered mutation (156)
      • engineered mutation (158)
      • engineered mutation (161-162)
      • engineered mutation (166)
      • engineered mutation (170)
      • engineered mutation (173)
  • Chain 'E':
    Compound: deoxynucleoside kinase
    Species: Drosophila melanogaster [TaxId:7227]
    Gene: dnk, CG5452
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9XZT6 (1-End)
      • initiating methionine (0)
      • engineered mutation (7)
      • engineered mutation (11)
      • engineered mutation (33)
      • engineered mutation (69)
      • engineered mutation (79)
      • engineered mutation (82)
      • engineered mutation (88)
      • engineered mutation (111)
      • engineered mutation (133)
      • engineered mutation (154)
      • engineered mutation (156)
      • engineered mutation (158)
      • engineered mutation (161-162)
      • engineered mutation (166)
      • engineered mutation (170)
      • engineered mutation (173)
    Domains in SCOPe 2.07: d6ybhe_
  • Chain 'F':
    Compound: deoxynucleoside kinase
    Species: Drosophila melanogaster [TaxId:7227]
    Gene: dnk, CG5452
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9XZT6 (1-End)
      • initiating methionine (0)
      • engineered mutation (7)
      • engineered mutation (11)
      • engineered mutation (33)
      • engineered mutation (69)
      • engineered mutation (79)
      • engineered mutation (82)
      • engineered mutation (88)
      • engineered mutation (111)
      • engineered mutation (133)
      • engineered mutation (154)
      • engineered mutation (156)
      • engineered mutation (158)
      • engineered mutation (161)
      • engineered mutation (166)
      • engineered mutation (170)
      • engineered mutation (173)
  • Heterogens: 4PC, GOL, SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6ybhB (B:)
    mkyaegtrpftiliegnigsgkttylnhfekykddiclltepvekwrnvngvnllelmyk
    dpkkwampfvsyvtltmlqmhtqptnkkvkimersifsarycfvenmrrngwleqgmynt
    leewykfieesihiqadliiylrtspevayerirkrgrpeeknvpleylqqlhqlhedwl
    ihqrrpqsckvlvldadlnlenigteyqrsessifdaissnqqp
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ybhB (B:)
    mkyaegtrpftiliegnigsgkttylnhfekykddiclltepvekwrnvngvnllelmyk
    dpkkwampfvsyvtltmlqmhtqptnkkvkimersifsarycfvenmrrngwleqgmynt
    leewykfieesihiqadliiylrtspevayerirkrgrpeeknvpleylqqlhqlhedwl
    ihqrrpqsckvlvldadlnlenigteyqrsessif
    

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >6ybhE (E:)
    mkyaegtrpftiliegnigsgkttylnhfekykddiclltepvekwrnvngvnllelmyk
    dpkkwampfvsyvtltmlqmhtqptnkkvkimersifsarycfvenmrrngwleqgmynt
    leewykfieesihiqadliiylrtspevayerirkrgrpeeknvpleylqqlhqlhedwl
    ihqrrpqsckvlvldadlnlenigteyqrsessifdaissnqqp
    

    Sequence, based on observed residues (ATOM records): (download)
    >6ybhE (E:)
    mkyaegtrpftiliegnigsgkttylnhfekykddiclltepvekwrnvngvnllelmyk
    dpkkwampfvsyvtltmlqmhtqptnkkvkimersifsarycfvenmrrngwleqgmynt
    leewykfieesihiqadliiylrtspevayerirkrgrpeeknvpleylqqlhqlhedwl
    ihqrrpqsckvlvldadlnlenigteyqr
    

  • Chain 'F':
    No sequence available.