PDB entry 5f39

View 5f39 on RCSB PDB site
Description: Crystal structure of human KDM4A in complex with compound 37
Class: oxidoreductase
Keywords: Epigenetics, Demethylase, Inhibitor, oxidoreductase
Deposited on 2015-12-02, released 2016-01-20
The last revision prior to the SCOPe 2.08 freeze date was dated 2016-03-09, with a file datestamp of 2016-03-04.
Experiment type: XRAY
Resolution: 2.65 Å
R-factor: N/A
AEROSPACI score: 0.18 (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: d5f39a_
  • 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: d5f39b_
  • 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: d5f39c_
  • 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: d5f39d_
  • Heterogens: ZN, 5UB, DMS, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5f39A (A:)
smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel

    Sequence, based on observed residues (ATOM records): (download) 
    >5f39A (A:)
npsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlvip
apiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknltfn
ppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwktsfawh
tedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlispl
mlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcsc
mvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5f39B (B:)
smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel

    Sequence, based on observed residues (ATOM records): (download) 
    >5f39B (B:)
sarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlvipap
iqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknltfnpp
iygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwktsfawhte
dmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplml
kkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscrk
dmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5f39C (C:)
smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel

    Sequence, based on observed residues (ATOM records): (download) 
    >5f39C (C:)
tlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddlv
ipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknlt
fnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfgmwktsfa
whtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlis
plmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlc
scrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >5f39D (D:)
smasesetlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasy
ddiddlvipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeeler
kywknltfnppiygadvngtlyekhvdewnigrlrtildlvekesgitiegvntpylyfg
mwktsfawhtedmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflr
hkmtlisplmlkkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwiey
gkqavlcscrkdmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaeflkesel

    Sequence, based on observed residues (ATOM records): (download) 
    >5f39D (D:)
etlnpsarimtfyptmeefrnfsryiayiesqgahraglakvvppkewkprasyddiddl
vipapiqqlvtgqsglftqyniqkkamtvrefrkiansdkyctprysefeelerkywknl
tfnppiygadvngtlyekhvdewnigrlrtildlvekesgvntpylyfgmwktsfawhte
dmdlysinylhfgepkswysvppehgkrlerlakgffpgsaqsceaflrhkmtlisplml
kkygipfdkvtqeagefmitfpygyhagfnhgfncaestnfatrrwieygkqavlcscrk
dmvkismdvfvrkfqperyklwkagkdntvidhtlptpeaaefl