PDB entry 5vmp

View 5vmp on RCSB PDB site
Description: Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714
Class: oxidoreductase/inhibitor
Keywords: KDM4, Inhibitor-complex, demethylase, epigenetics, OXIDOREDUCTASE-INHIBITOR complex
Deposited on 2017-04-28, released 2017-09-27
The last revision prior to the SCOPe 2.08 freeze date was dated 2017-09-27, with a file datestamp of 2017-09-22.
Experiment type: XRAY
Resolution: 2.48 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 2.08: d5vmpa_
  • 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 2.08: d5vmpb_
  • 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 2.08: d5vmpc_
  • 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 2.08: d5vmpd_
  • Heterogens: NI, ZN, 9FJ, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5vmpA (A:)
mghhhhhhgsgenlyfqsnsetlnpsarimtfyptmeefrnfsryiayiesqgahragla
kvvppkewkprasyddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdk
yctprysefeelerkywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesg
itiegvntpylyfgmwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakg
ffpgsaqsceaflrhkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfnc
aestnfatrrwieygkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtl
ptpeaaefl

    Sequence, based on observed residues (ATOM records): (download) 
    >5vmpA (A:)
setlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddidd
lvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywkn
ltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwkts
fawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtl
isplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqav
lcscrvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5vmpB (B:)
mghhhhhhgsgenlyfqsnsetlnpsarimtfyptmeefrnfsryiayiesqgahragla
kvvppkewkprasyddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdk
yctprysefeelerkywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesg
itiegvntpylyfgmwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakg
ffpgsaqsceaflrhkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfnc
aestnfatrrwieygkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtl
ptpeaaefl

    Sequence, based on observed residues (ATOM records): (download) 
    >5vmpB (B:)
setlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddidd
lvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywkn
ltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwkts
fawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtl
isplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqav
lcscrvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5vmpC (C:)
mghhhhhhgsgenlyfqsnsetlnpsarimtfyptmeefrnfsryiayiesqgahragla
kvvppkewkprasyddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdk
yctprysefeelerkywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesg
itiegvntpylyfgmwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakg
ffpgsaqsceaflrhkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfnc
aestnfatrrwieygkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtl
ptpeaaefl

    Sequence, based on observed residues (ATOM records): (download) 
    >5vmpC (C:)
arimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlvipapi
qqlvtgqsglftqyniqkkamtvrefrkiansdkyctpryfeelerkywknltfnppiyg
advngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwktsfawhtedmd
lysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplmlkky
gipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscrkism
dvfvrkfqperyklwkagktvidhtlptpeaaefl

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >5vmpD (D:)
mghhhhhhgsgenlyfqsnsetlnpsarimtfyptmeefrnfsryiayiesqgahragla
kvvppkewkprasyddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdk
yctprysefeelerkywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesg
itiegvntpylyfgmwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakg
ffpgsaqsceaflrhkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfnc
aestnfatrrwieygkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtl
ptpeaaefl

    Sequence, based on observed residues (ATOM records): (download) 
    >5vmpD (D:)
setlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddidd
lvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywkn
ltfnppiygadvngtlyekhvdewnigrlrtildlvekesgvntpylyfgmwktsfawht
edmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplm
lkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscr
vkismdvfvrkfqperyklwkagkdntvidhtlptpeaaef