Structure of PDB 2p5b Chain A

Receptor sequence

>2p5bA (length=347) Species: 9606 (Homo sapiens)

ASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPK
EWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIA
NSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIG
RLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLH
FGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLK
KYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGK
QAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTP

3D structure

• PDB: 2p5b Structural basis of the recognition of a methylated histone tail by JMJD2A.
• Chain: A
• Resolution: 1.99 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): G170 Y177 H188 E190 H276 S288
• Catalytic site (residue number reindexed from 1): G169 Y176 H187 E189 H275 S287
• 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 T289 N290 R309 D311 V313 K314 I315 S316	I70 N85 I86 Q87 D134 I165 I167 E168 G169 Y174 Y176 M241 S287 T288 N289 R308 D310 V312 K313 I314 S315
BS02	ZN	A	C234 H240 C306 C308	C233 H239 C305 C307
BS03	FE2	A	H188 E190 H276	H187 E189 H275
BS04	OGA	A	Y132 F185 H188 E190 S196 N198 W208 H276	Y131 F184 H187 E189 S195 N197 W207 H275	BindingDB: IC50=250000nM
BS05	OXY	A	E190 K241	E189 K240
BS06	OXY	A	H188 E190	H187 E189

External links

• PDB: RCSB:2p5b, PDBe:2p5b, PDBj:2p5b
• PDBsum: 2p5b
• PubMed: 17567753
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)