Structure of PDB 5ly2 Chain D

Receptor sequence
>5ly2D (length=347) Species: 9606 (Homo sapiens) [Search protein sequence]
LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRA
SYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYC
TPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTIL
DLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKS
WYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPF
DKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCS
CRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
3D structure
PDB5ly2 Highly selective inhibition of histone demethylases by de novo macrocyclic peptides.
ChainD
Resolution2.43 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) 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 D I87 Q88 K89 K90 I80 Q81 K82 K83
BS02 peptide D A69 N86 D135 G170 Y175 Y177 H240 K241 M242 S288 N290 C308 R309 D311 M312 A62 N79 D128 G163 Y168 Y170 H233 K234 M235 S281 N283 C301 R302 D304 M305
BS03 ZN D C234 H240 C306 C308 C227 H233 C299 C301
External links
PDB RCSB:5ly2, PDBe:5ly2, PDBj:5ly2
PDBsum5ly2
PubMed28382930
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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