Structure of PDB 2ybk Chain B

Receptor sequence
>2ybkB (length=349) Species: 9606 (Homo sapiens) [Search protein sequence]
TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPR
ASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKY
CTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTI
LDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPK
SWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIP
FDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLC
SCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK
3D structure
PDB2ybk The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases.
ChainB
Resolution2.4 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 ZN B C234 H240 C306 C228 H234 C300
BS02 2HG B Y132 Y177 F185 H188 S196 N198 K206 W208 H276 Y126 Y171 F179 H182 S190 N192 K200 W202 H270 MOAD: ic50=24uM
BindingDB: IC50=24000nM
External links
PDB RCSB:2ybk, PDBe:2ybk, PDBj:2ybk
PDBsum2ybk
PubMed21460794
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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