Structure of PDB 2ybs Chain A

Receptor sequence
>2ybsA (length=348) Species: 9606 (Homo sapiens) [Search protein sequence]
LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRA
SYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYC
TPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTIL
DLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKS
WYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPF
DKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCS
CRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK
3D structure
PDB2ybs The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases.
ChainA
Resolution2.32 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) G163 Y170 H181 E183 H269 S281
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 peptide A I71 N86 I87 Q88 D135 I166 I168 E169 G170 Y175 Y177 M242 S288 N290 D311 V313 K314 S316 I64 N79 I80 Q81 D128 I159 I161 E162 G163 Y168 Y170 M235 S281 N283 D304 V306 K307 S309
BS02 ZN A C234 H240 C306 C308 C227 H233 C299 C301
BS03 S2G A Y132 F185 H188 N198 K206 H276 Y125 F178 H181 N191 K199 H269 PDBbind-CN: -logKd/Ki=4.59,IC50=26uM
BindingDB: IC50=26000nM
External links
PDB RCSB:2ybs, PDBe:2ybs, PDBj:2ybs
PDBsum2ybs
PubMed21460794
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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