Structure of PDB 5lw9 Chain A

Receptor sequence

>5lw9A (length=456) Species: 9606 (Homo sapiens) [Search protein sequence]

MFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPF
ACDVDKLHFTPRIQRLNELEAQTRVKARDYTLRTFGEMADAFKSDYFNMP
VHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGIKLS
PEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCW
HIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDL
LHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAE
AVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVA
STVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTT
CFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNAL
KLRAES

3D structure

PDB

5lw9 Crystal structure of human JARID1B in complex with S40563a

Chain

Resolution

2.3 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	G481 Y488 H499 E501 H587 A599
Catalytic site (residue number reindexed from 1)	G183 Y190 H201 E203 H289 A301
Enzyme Commision number	1.14.11.67: [histone H3]-trimethyl-L-lysine(4) 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	ZN	A	C692 C695 C715 H718	C394 C397 C417 H420
BS02	MN	A	L90 N91 T416	L66 N67 T119
BS03	5UJ	A	Y425 D428 W486 Y488 F496 H499 E501 K517 W519 H587	Y128 D131 W188 Y190 F198 H201 E203 K219 W221 H289	BindingDB: IC50=14nM
BS04	MN	A	H499 E501 H587	H201 E203 H289

External links

PDB	RCSB:5lw9, PDBe:5lw9, PDBj:5lw9
PDBsum	5lw9
PubMed
UniProt	Q9UGL1\|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)

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