Structure of PDB 5l3e Chain A

Receptor sequence
>5l3eA (length=666) Species: 9606 (Homo sapiens) [Search protein sequence]
PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQL
WLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRI
KPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATF
RKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV
PKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE
KHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKP
PRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVY
LSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNG
YSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDA
VLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVF
WDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISD
DVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSG
NDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLR
EAGRIADQFLGAMYTL
3D structure
PDB5l3e Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.
ChainA
Resolution2.8 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
Catalytic site (residue number reindexed from 1) T165
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 V333 V590 L625 W756 S760 Y761 G800 E801 T810 V811 G115 G117 S119 E138 A139 R140 G145 R146 G160 A161 V163 V420 L455 W586 S590 Y591 G630 E631 T640 V641
BS02 E11 A L386 N535 L536 A539 W552 H564 W695 L216 N365 L366 A369 W382 H394 W525 PDBbind-CN: -logKd/Ki=6.18,Kd=660nM
BindingDB: Kd=243nM
BS03 E11 A N383 E387 S390 D556 E559 N213 E217 S220 D386 E389 PDBbind-CN: -logKd/Ki=6.18,Kd=660nM
BindingDB: Kd=243nM
BS04 E11 A E559 G562 E389 G392 PDBbind-CN: -logKd/Ki=6.18,Kd=660nM
BindingDB: Kd=243nM
BS05 E11 A D557 E559 D387 E389 PDBbind-CN: -logKd/Ki=6.18,Kd=660nM
BindingDB: Kd=243nM
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:5l3e, PDBe:5l3e, PDBj:5l3e
PDBsum5l3e
PubMed27626075
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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