PDB entry 5ly2

View 5ly2 on RCSB PDB site
Description: jmjd2a/ kdm4a complexed with ni(ii), nog and macrocyclic peptide inhibitor cp2_r6kme3 (13-mer)
Deposited on 2016-09-23, released 2017-04-12
The last revision was dated 2019-06-12, with a file datestamp of 2019-06-07.
Experiment type: XRAY
Resolution: 2.4299999999999997 Å
R-factor: N/A
AEROSPACI score: 0.22 (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):
  • 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):
  • 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):
  • 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):
  • Chain 'E':
    Compound: CP2_R6Kme3
    Species: artificial sequences, synthetic [TaxId:81077]
    Database cross-references and differences (RAF-indexed):
    • PDB 5LY2 (0-13)
  • Chain 'F':
    Compound: CP2_R6Kme3
    Species: artificial sequences, synthetic [TaxId:81077]
    Database cross-references and differences (RAF-indexed):
    • PDB 5LY2
  • Chain 'G':
    Compound: CP2_R6Kme3
    Species: artificial sequences, synthetic [TaxId:81077]
    Database cross-references and differences (RAF-indexed):
    • PDB 5LY2 (0-13)
  • Chain 'H':
    Compound: CP2_R6Kme3
    Species: artificial sequences, synthetic [TaxId:81077]
    Database cross-references and differences (RAF-indexed):
    • PDB 5LY2
  • Heterogens: NI, ZN, OGA, GOL, CL, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >5ly2A (A:)
    mhhhhhhssgvdlgtenlyfqsmasesetlnpsarimtfyptmeefrnfsryiayiesqg
    ahraglakvvppkewkprasyddiddlvipapiqqlvtgqsglftqyniqkkamtvrefr
    kiansdkyctprysefeelerkywknltfnppiygadvngtlyekhvdewnigrlrtild
    lvekesgitiegvntpylyfgmwktsfawhtedmdlysinylhfgepkswysvppehgkr
    lerlakgffpgsaqsceaflrhkmtlisplmlkkygipfdkvtqeagefmitfpygyhag
    fnhgfncaestnfatrrwieygkqavlcscrkdmvkismdvfvrkfqperyklwkagkdn
    tvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records):
    >5ly2A (A:)
    tlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlv
    ipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknlt
    fnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwktsfa
    whtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlis
    plmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlc
    scrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >5ly2B (B:)
    mhhhhhhssgvdlgtenlyfqsmasesetlnpsarimtfyptmeefrnfsryiayiesqg
    ahraglakvvppkewkprasyddiddlvipapiqqlvtgqsglftqyniqkkamtvrefr
    kiansdkyctprysefeelerkywknltfnppiygadvngtlyekhvdewnigrlrtild
    lvekesgitiegvntpylyfgmwktsfawhtedmdlysinylhfgepkswysvppehgkr
    lerlakgffpgsaqsceaflrhkmtlisplmlkkygipfdkvtqeagefmitfpygyhag
    fnhgfncaestnfatrrwieygkqavlcscrkdmvkismdvfvrkfqperyklwkagkdn
    tvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records):
    >5ly2B (B:)
    psarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlvipa
    piqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknltfnp
    piygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwktsfawht
    edmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplm
    lkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscr
    kdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >5ly2C (C:)
    mhhhhhhssgvdlgtenlyfqsmasesetlnpsarimtfyptmeefrnfsryiayiesqg
    ahraglakvvppkewkprasyddiddlvipapiqqlvtgqsglftqyniqkkamtvrefr
    kiansdkyctprysefeelerkywknltfnppiygadvngtlyekhvdewnigrlrtild
    lvekesgitiegvntpylyfgmwktsfawhtedmdlysinylhfgepkswysvppehgkr
    lerlakgffpgsaqsceaflrhkmtlisplmlkkygipfdkvtqeagefmitfpygyhag
    fnhgfncaestnfatrrwieygkqavlcscrkdmvkismdvfvrkfqperyklwkagkdn
    tvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records):
    >5ly2C (C:)
    setlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddidd
    lvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywkn
    ltfnppiygadvngtlyekhvdewnigrlrtildlvegvntpylyfgmwktsfawhtedm
    dlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplmlkk
    ygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscrkdm
    vkismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >5ly2D (D:)
    mhhhhhhssgvdlgtenlyfqsmasesetlnpsarimtfyptmeefrnfsryiayiesqg
    ahraglakvvppkewkprasyddiddlvipapiqqlvtgqsglftqyniqkkamtvrefr
    kiansdkyctprysefeelerkywknltfnppiygadvngtlyekhvdewnigrlrtild
    lvekesgitiegvntpylyfgmwktsfawhtedmdlysinylhfgepkswysvppehgkr
    lerlakgffpgsaqsceaflrhkmtlisplmlkkygipfdkvtqeagefmitfpygyhag
    fnhgfncaestnfatrrwieygkqavlcscrkdmvkismdvfvrkfqperyklwkagkdn
    tvidhtlptpeaaeflkesel
    

    Sequence, based on observed residues (ATOM records):
    >5ly2D (D:)
    lnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlvi
    papiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknltf
    nppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwktsfaw
    htedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisp
    lmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcs
    crkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records:
    >5ly2E (E:)
    xyvyntksgwrwyt
    

  • Chain 'F':
    Sequence, based on SEQRES records:
    >5ly2F (F:)
    xyvyntksgwrwyt
    

    Sequence, based on observed residues (ATOM records):
    >5ly2F (F:)
    yntksgwr
    

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records:
    >5ly2G (G:)
    xyvyntksgwrwyt
    

  • Chain 'H':
    Sequence, based on SEQRES records:
    >5ly2H (H:)
    xyvyntksgwrwyt
    

    Sequence, based on observed residues (ATOM records):
    >5ly2H (H:)
    yntksgwr