BioLiP

Structure of PDB 5ly2 Chain B

Receptor sequence

>5ly2B (length=345) Species: 9606 (Homo sapiens) [Search protein sequence]

PSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASY
DDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTP
RYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDL
VEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWY
SVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDK
VTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCR
KDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL

3D structure

PDB

5ly2 Highly selective inhibition of histone demethylases by de novo macrocyclic peptides.

Chain

Resolution

2.43 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)	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)
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)

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