Structure of PDB 5ly2 Chain B

Receptor sequence

>5ly2B (length=345) Species: 9606 (Homo sapiens)

PSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASY
DDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTP
RYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDL
VEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWY
SVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDK
VTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCR
KDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL

3D structure

• PDB: 5ly2 Highly selective inhibition of histone demethylases by de novo macrocyclic peptides.
• Chain: B
• Resolution: 2.43 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): G170 Y177 H188 E190 H276 S288
• Catalytic site (residue number reindexed from 1): G161 Y168 H179 E181 H267 S279
• 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	I87 Q88 K89 K90	I78 Q79 K80 K81
BS02	peptide	B	A69 N86 D135 G170 Y177 E190 H240 K241 T289 N290 C308 D311 M312	A60 N77 D126 G161 Y168 E181 H231 K232 T280 N281 C299 D302 M303
BS03	ZN	B	C234 H240 C306 C308	C225 H231 C297 C299

External links

• PDB: RCSB:5ly2, PDBe:5ly2, PDBj:5ly2
• PDBsum: 5ly2
• PubMed: 28382930
• UniProt: O75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)