Structure of PDB 4lxl Chain A

Receptor sequence

>4lxlA (length=329) Species: 9606 (Homo sapiens)

QNPSCKIMTFRPTMEEFKDFNKYVAYIESQGAHRAGLAKIIPPKEWKPRQ
TYDDIDDVVIPAPIQQVVTGQSGLFTQYNIQKKAMTVGEYRRLANSEKYC
TPRHQDFDDLERKYWKNLTFVSPIYGADISGSLYDDDVAQWNIGSLRTIL
DMVERECGTIIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKS
WYAIPPEHGKRLERLAIGFFPGSSQGCDAFLRHKMTLISPIILKKYGIPF
SRITQEAGEFMITFPYGYHAGFNHGFNCAESTNFATLRWIDYGKVATQCT
CRKDMVKISMDVFVRILQPERYELWKQGK

3D structure

• PDB: 4lxl Crystal structure of JMJD2B complexed with pyridine-2,4-dicarboxylic acid and H3K9me3
• Chain: A
• Resolution: 1.87 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D136 G171 Y178 H189 E191 H277 S289 N291
• Catalytic site (residue number reindexed from 1): D128 G163 Y170 H181 E183 H269 S281 N283
• Enzyme Commision number: 1.14.11.66: [histone H3]-trimethyl-L-lysine(9) 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	Y86 N87 D136 E170 G171 Y176 Y178 H241 K242 M243 S289 N291 M313	Y78 N79 D128 E162 G163 Y168 Y170 H233 K234 M235 S281 N283 M305
BS02	PD2	A	Y133 Y178 F186 H189 E191 K207 W209 K242 H277	Y125 Y170 F178 H181 E183 K199 W201 K234 H269
BS03	ZN	A	C235 H241 C307 C309	C227 H233 C299 C301

External links

• PDB: RCSB:4lxl, PDBe:4lxl, PDBj:4lxl
• PDBsum: 4lxl
• UniProt: O94953|KDM4B_HUMAN Lysine-specific demethylase 4B (Gene Name=KDM4B)