Structure of PDB 2ybp Chain B

Receptor sequence

>2ybpB (length=353) Species: 9606 (Homo sapiens)

SESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKE
WKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIAN
SDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGR
LRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHF
GEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKK
YGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQ
AVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAE
FLK

3D structure

• PDB: 2ybp The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases.
• Chain: B
• Resolution: 2.02 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): G170 Y177 H188 E190 H276 S288
• Catalytic site (residue number reindexed from 1): G168 Y175 H186 E188 H274 S286
• 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	B	I71 N86 I87 D135 I166 E169 G170 Y175 Y177 M242 S288 N290 D311 V313 K314 S316	I69 N84 I85 D133 I164 E167 G168 Y173 Y175 M240 S286 N288 D309 V311 K312 S314
BS02	ZN	B	C234 H240 C306 C308	C232 H238 C304 C306
BS03	2HG	B	Y132 F185 H188 S196 N198 K206 W208 H276 S288	Y130 F183 H186 S194 N196 K204 W206 H274 S286	BindingDB: IC50=24000nM

External links

• PDB: RCSB:2ybp, PDBe:2ybp, PDBj:2ybp
• PDBsum: 2ybp
• PubMed: 21460794
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)