PDB entry 5f3g

View 5f3g on RCSB PDB site
Description: Crystal structure of human KDM4A in complex with compound 53a
Class: oxidoreductase
Keywords: Epigenetics, Demethylase, Inhibitor, oxidoreductase
Deposited on 2015-12-02, released 2016-01-20
The last revision prior to the SCOPe 2.06 freeze date was dated 2016-03-09, with a file datestamp of 2016-03-04.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: N/A
AEROSPACI score: 0.21 (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 2.06: d5f3ga_
  • 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 2.06: d5f3gb_
  • 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 2.06: d5f3gc_
  • 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 2.06: d5f3gd_
  • Heterogens: ZN, 5UL, DMS, CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5f3gA (A:)
    smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
    ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
    kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
    mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
    hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
    gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records): (download)
    >5f3gA (A:)
    lnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlvi
    papiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknltf
    nppiygadvngtlyekhvdewnigrlrtildlvekesgvntpylyfgmwktsfawhtedm
    dlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplmlkk
    ygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscmvki
    smdvfvrkfqperyklwkagkdntvidhtlptpeaaefl
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5f3gB (B:)
    smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
    ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
    kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
    mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
    hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
    gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records): (download)
    >5f3gB (B:)
    npsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlvip
    apiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknltfn
    ppiygadvngtlyekhvdewnigrlrtildlvegvntpylyfgmwktsfawhtedmdlys
    inylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplmlkkygip
    fdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscrmvkismd
    vfvrkfqperyklwkagkdntvidhtlptpeaaef
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5f3gC (C:)
    smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
    ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
    kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
    mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
    hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
    gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records): (download)
    >5f3gC (C:)
    lnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlvi
    papiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknltf
    nppiygadvngtlyekhvdewnigrlrtildlvegvntpylyfgmwktsfawhtedmdly
    sinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplmlkkygi
    pfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscrmvkism
    dvfvrkfqperyklwkagkdntvidhtlptpeaaefl
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5f3gD (D:)
    smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
    ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
    kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
    mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
    hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
    gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records): (download)
    >5f3gD (D:)
    sarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlvipap
    iqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknltfnpp
    iygadvngtlyekhvdewnigrlrtildlvekesgitivntpylyfgmwktsfawhtedm
    dlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplmlkk
    ygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscmvki
    smdvfvrkfqperyklwkagkdntvidhtlptpeaaefl