Structure of PDB 2ybs Chain A Binding Site BS01

Receptor Information

>2ybs Chain A (length=348) Species: 9606 (Homo sapiens)

LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRA
SYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYC
TPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTIL
DLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKS
WYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPF
DKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCS
CRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK

Ligand information

>2ybs Chain C (length=12) Species: 9606 (Homo sapiens)

PATGGVKKPHRY

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ybs The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases.
• Resolution: 2.32 Å
• Binding residue (original residue number in PDB): I71 N86 I87 Q88 D135 I166 I168 E169 G170 Y175 Y177 M242 S288 N290 D311 V313 K314 S316
• Binding residue (residue number reindexed from 1): I64 N79 I80 Q81 D128 I159 I161 E162 G163 Y168 Y170 M235 S281 N283 D304 V306 K307 S309

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.

External links

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