Structure of PDB 5yjb Chain A

Receptor sequence

>5yjbA (length=661) Species: 9606 (Homo sapiens) [Search protein sequence]

SGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLW
LDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIK
PLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFR
KGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVP
KEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEK
HVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPP
RDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYL
SSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGY
SCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAV
LCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFW
DPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDD
VIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGN
DYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLRE
AGRIADQFLGA

3D structure

PDB

5yjb Crystal Structure of LSD1 in Complex with 4-[5-(Piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile.

Chain

Resolution

2.96 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	T335 D553 K661
Catalytic site (residue number reindexed from 1)	T164 D382 K490
Enzyme Commision number	1.14.99.66: [histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent 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	FAD	A	G285 G287 S289 E308 A309 R310 G315 R316 G330 A331 M332 V333 A589 V590 L625 P626 W751 W756 S760 Y761 G800 E801 T810 V811	G114 G116 S118 E137 A138 R139 G144 R145 G159 A160 M161 V162 A418 V419 L454 P455 W580 W585 S589 Y590 G629 E630 T639 V640
BS02	8WC	A	M332 F538 D555 L659 K661 W695 A809	M161 F367 D384 L488 K490 W524 A638	PDBbind-CN: -logKd/Ki=7.54,Ki=29nM BindingDB: Ki=29nM

Gene Ontology

	Molecular Function
GO:0016491	oxidoreductase activity
GO:0050660	flavin adenine dinucleotide binding

	Biological Process
GO:0006355	regulation of DNA-templated transcription

	Cellular Component
GO:0005634	nucleus

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:5yjb, PDBe:5yjb, PDBj:5yjb
PDBsum	5yjb
PubMed	29949906
UniProt	O60341\|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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