PDB entry 6hgt

View 6hgt on RCSB PDB site
Description: Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation
Class: oxidoreductase
Keywords: Histone demethylase, Inhibitor, transcription, OXIDOREDUCTASE
Deposited on 2018-08-23, released 2019-09-04
The last revision prior to the SCOPe 2.07 freeze date was dated 2019-09-04, with a file datestamp of 2019-08-30.
Experiment type: XRAY
Resolution: 2.33 Å
R-factor: N/A
AEROSPACI score: 0.24 (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: d6hgta_
  • 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: d6hgtb_
  • 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: d6hgtc_
  • 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: d6hgtd_
  • Chain 'E':
    Compound: Histone H3.3
    Species: Homo sapiens [TaxId:9606]
    Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B
    Database cross-references and differences (RAF-indexed):
    • Uniprot P84243
      • engineered mutation (6)
  • Chain 'F':
    Compound: Histone H3.3
    Species: Homo sapiens [TaxId:9606]
    Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B
    Database cross-references and differences (RAF-indexed):
    • Uniprot P84243
      • engineered mutation (6)
  • Chain 'G':
    Compound: Histone H3.3
    Species: Homo sapiens [TaxId:9606]
    Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B
    Database cross-references and differences (RAF-indexed):
    • Uniprot P84243
      • engineered mutation (6)
  • Chain 'H':
    Compound: Histone H3.3
    Species: Homo sapiens [TaxId:9606]
    Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B
    Database cross-references and differences (RAF-indexed):
    • Uniprot P84243
      • engineered mutation (6)
  • Heterogens: OGA, ZN, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6hgtA (A:)
    smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
    ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
    kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
    mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
    hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
    gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records): (download)
    >6hgtA (A:)
    setlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddidd
    lvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywkn
    ltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwkts
    fawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtl
    isplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqav
    lcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6hgtB (B:)
    smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
    ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
    kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
    mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
    hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
    gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records): (download)
    >6hgtB (B:)
    tlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlv
    ipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknlt
    fnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwktsfa
    whtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlis
    plmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlc
    scrmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaef
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6hgtC (C:)
    smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
    ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
    kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
    mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
    hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
    gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records): (download)
    >6hgtC (C:)
    etlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddl
    vipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknl
    tfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwktsf
    awhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtli
    splmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavl
    cscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaef
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6hgtD (D:)
    smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
    ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
    kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
    mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
    hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
    gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records): (download)
    >6hgtD (D:)
    psarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlvipa
    piqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknltfnp
    piygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwktsfawht
    edmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplm
    lkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscr
    kmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaae
    

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.