Structure of PDB 5tvr Chain B

Receptor sequence
>5tvrB (length=346) Species: 9606 (Homo sapiens) [Search protein sequence]
TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPR
ASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKY
CTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTI
LDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPK
SWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIP
FDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLC
SCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAE
3D structure
PDB5tvr The small molecule JIB-04 disrupts O2 binding in the Fe-dependent histone demethylase KDM4A/JMJD2A.
ChainB
Resolution2.093 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G164 Y171 H182 E184 H270 S282
Enzyme Commision number 1.14.11.66: [histone H3]-trimethyl-L-lysine(9) demethylase.
1.14.11.69: [histone H3]-trimethyl-L-lysine(36) demethylase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 AKG B Y132 F185 H188 S196 N198 K206 H276 Y126 F179 H182 S190 N192 K200 H270
BS02 ZN B C234 H240 C306 C308 C228 H234 C300 C302
External links
PDB RCSB:5tvr, PDBe:5tvr, PDBj:5tvr
PDBsum5tvr
PubMed28144654
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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