PDB entry 5f3c

View 5f3c on RCSB PDB site
Description: Crystal structure of human KDM4A in complex with compound 52d
Class: oxidoreductase
Keywords: Epigenetics, Demethylase, Inhibitor, oxidoreductase
Deposited on 2015-12-02, released 2016-01-20
The last revision prior to the SCOPe 2.07 freeze date was dated 2016-03-09, with a file datestamp of 2016-03-04.
Experiment type: XRAY
Resolution: 2.06 Å
R-factor: N/A
AEROSPACI score: 0.3 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: lysine-specific demethylase 4a
    Species: Homo sapiens [TaxId:9606]
    Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5f3ca_
  • Chain 'B':
    Compound: lysine-specific demethylase 4a
    Species: Homo sapiens [TaxId:9606]
    Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5f3cb_
  • Chain 'C':
    Compound: lysine-specific demethylase 4a
    Species: Homo sapiens [TaxId:9606]
    Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5f3cc_
  • Chain 'D':
    Compound: lysine-specific demethylase 4a
    Species: Homo sapiens [TaxId:9606]
    Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5f3cd_
  • Heterogens: ZN, 5U8, DMS, GOL, CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5f3cA (A:)
    smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
    ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
    kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
    mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
    hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
    gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records): (download)
    >5f3cA (A:)
    psarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlvipa
    piqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknltfnp
    piygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwktsfawht
    edmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplm
    lkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscr
    mvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5f3cB (B:)
    smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
    ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
    kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
    mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
    hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
    gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records): (download)
    >5f3cB (B:)
    psarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlvipa
    piqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknltfnp
    piygadvngtlyekhvdewnigrlrtildlvegvntpylyfgmwktsfawhtedmdlysi
    nylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplmlkkygipf
    dkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscrkdmvkism
    dvfvrkfqperyklwkagkdntvidhtlptpeaaefl
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5f3cC (C:)
    smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
    ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
    kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
    mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
    hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
    gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records): (download)
    >5f3cC (C:)
    etlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddl
    vipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknl
    tfnppiygadvngtlyekhvdewnigrlrtildlvevntpylyfgmwktsfawhtedmdl
    ysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplmlkkyg
    ipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscrkdmvk
    ismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5f3cD (D:)
    smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
    ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
    kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
    mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
    hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
    gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records): (download)
    >5f3cD (D:)
    setlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddidd
    lvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywkn
    ltfnppiygadvngtlyekhvdewnigrlrtildlvegvntpylyfgmwktsfawhtedm
    dlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplmlkk
    ygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscrkdm
    vkismdvfvrkfqperyklwkagkdntvidhtlptpeaaef