PDB entry 5k1i

View 5k1i on RCSB PDB site
Description: PDE4 crystal structure in complex with small molecule inhibitor
Class: hydrolase
Keywords: phosphodiesterases, inhibitor, Hydrolase
Deposited on 2016-05-18, released 2016-12-21
The last revision prior to the SCOPe 2.07 freeze date was dated 2016-12-21, with a file datestamp of 2016-12-16.
Experiment type: XRAY
Resolution: 2.61 Å
R-factor: N/A
AEROSPACI score: 0.19 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE4D, DPDE3
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k1ia_
  • Chain 'B':
    Compound: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE4D, DPDE3
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k1ib_
  • Chain 'C':
    Compound: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE4D, DPDE3
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k1ic_
  • Chain 'D':
    Compound: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE4D, DPDE3
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k1id_
  • Chain 'E':
    Compound: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE4D, DPDE3
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k1ie_
  • Chain 'F':
    Compound: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE4D, DPDE3
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k1if_
  • Chain 'G':
    Compound: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE4D, DPDE3
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k1ig_
  • Chain 'H':
    Compound: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
    Species: Homo sapiens [TaxId:9606]
    Gene: PDE4D, DPDE3
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5k1ih_
  • Heterogens: 6PT, ZN, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5k1iA (A:)
    teqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlity
    lmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhp
    gvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvi
    divlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcadlsnptkp
    lqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwa
    dlvhpdaqdildtlednrewyqstip
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k1iA (A:)
    eqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlityl
    mtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhpg
    vsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvid
    ivlatdmskhmnlladlktmvetkkvtvllldnysdriqvlqnmvhcadlsnptkplqly
    rqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwadlvh
    pdaqdildtlednrewyqstip
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5k1iB (B:)
    teqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlity
    lmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhp
    gvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvi
    divlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcadlsnptkp
    lqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwa
    dlvhpdaqdildtlednrewyqstip
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5k1iC (C:)
    teqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlity
    lmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhp
    gvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvi
    divlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcadlsnptkp
    lqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwa
    dlvhpdaqdildtlednrewyqstip
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k1iC (C:)
    eqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlityl
    mtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhpg
    vsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvid
    ivlatdmskhmnlladlktmvetkkvvllldnysdriqvlqnmvhcadlsnptkplqlyr
    qwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwadlvhp
    daqdildtlednrewyqstip
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5k1iD (D:)
    teqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlity
    lmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhp
    gvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvi
    divlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcadlsnptkp
    lqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwa
    dlvhpdaqdildtlednrewyqstip
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5k1iE (E:)
    teqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlity
    lmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhp
    gvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvi
    divlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcadlsnptkp
    lqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwa
    dlvhpdaqdildtlednrewyqstip
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k1iE (E:)
    eqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlityl
    mtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhpg
    vsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvid
    ivlatdmskhmnlladlktmvetkkvvllldnysdriqvlqnmvhcadlsnptkplqlyr
    qwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwadlvhp
    daqdildtlednrewyqstip
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5k1iF (F:)
    teqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlity
    lmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhp
    gvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvi
    divlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcadlsnptkp
    lqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwa
    dlvhpdaqdildtlednrewyqstip
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5k1iG (G:)
    teqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlity
    lmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhp
    gvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvi
    divlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcadlsnptkp
    lqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwa
    dlvhpdaqdildtlednrewyqstip
    

    Sequence, based on observed residues (ATOM records): (download)
    >5k1iG (G:)
    eqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlityl
    mtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhpg
    vsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvid
    ivlatdmskhmnlladlktmvetkkvtvllldnysdriqvlqnmvhcadlsnptkplqly
    rqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwadlvh
    pdaqdildtlednrewyqstip
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5k1iH (H:)
    teqedvlakeledvnkwglhvfriaelsgnrpltvimhtifqerdllktfkipvdtlity
    lmtledhyhadvayhnnihaadvvqsthvllstpaleavftdleilaaifasaihdvdhp
    gvsnqflintnselalmyndssvlenhhlavgfkllqeencdifqnltkkqrqslrkmvi
    divlatdmskhmnlladlktmvetkkvtssgvllldnysdriqvlqnmvhcadlsnptkp
    lqlyrqwtdrimeeffrqgdrerergmeispmcdkhnasveksqvgfidyivhplwetwa
    dlvhpdaqdildtlednrewyqstip