Structure of PDB 7cdd Chain A

Receptor sequence

>7cddA (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

7cdd 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

2.76 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	peptide	A	C360 D375 E379 N535 L536 F538 A539 W552 D553 D556 E559 L677 Y761 A809	C189 D204 E208 N364 L365 F367 A368 W381 D382 D385 E388 L506 Y590 A638
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	G114 G116 S118 E137 A138 R139 G144 R145 G159 A160 M161 V162 V419 L454 W585 S589 Y590 G629 E630 A638 T639 V640

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

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