Structure of PDB 7cdf Chain A

Receptor sequence

>7cdfA (length=663) Species: 9606 (Homo sapiens) [Search protein sequence]

HMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQ
LWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKR
IKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVAT
FRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQA
VPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQ
EKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVK
PPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDV
YLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRN
GYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCD
AVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRV
FWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENIS
DDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSS
GNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGL
REAGRIADQFLGA

3D structure

PDB

7cdf Structure-Based Identification of Potent Lysine-Specific Demethylase 1 Inhibitor Peptides and Temporary Cyclization to Enhance Proteolytic Stability and Cell Growth-Inhibitory Activity.

Chain

Resolution

2.68 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)	T166 D384 K492
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	peptide	A	C360 D375 E379 N383 E387 N535 L536 F538 A539 W552 D553 D556 E559 Y761 A809	C191 D206 E210 N214 E218 N366 L367 F369 A370 W383 D384 D387 E390 Y592 A640
BS02	FAD	A	G285 G287 S289 E308 A309 R310 G315 R316 G330 A331 M332 V333 V590 L625 W756 S760 Y761 G800 E801 A809 T810 V811	G116 G118 S120 E139 A140 R141 G146 R147 G161 A162 M163 V164 V421 L456 W587 S591 Y592 G631 E632 A640 T641 V642

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:7cdf, PDBe:7cdf, PDBj:7cdf
PDBsum	7cdf
PubMed	33754721
UniProt	O60341\|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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