Structure of PDB 5h6r Chain A

Receptor sequence

>5h6rA (length=662) Species: 9606 (Homo sapiens) [Search protein sequence]

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

3D structure

PDB

5h6r Development and crystallographic evaluation of histone H3 peptide with N-terminal serine substitution as a potent inhibitor of lysine-specific demethylase 1.

Chain

Resolution

2.6 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	I356 C360 D375 E379 N383 L386 N535 L536 A539 W552 D553 D555 D556 E559 H564 L677 Y761	I185 C189 D204 E208 N212 L215 N364 L365 A368 W381 D382 D384 D385 E388 H393 L506 Y590
BS02	FAD	A	G285 G287 S289 E308 A309 R310 G315 R316 G330 A331 V333 V590 L625 P626 W751 W756 S760 Y761 G800 E801 A809 T810 V811	G114 G116 S118 E137 A138 R139 G144 R145 G159 A160 V162 V419 L454 P455 W580 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:5h6r, PDBe:5h6r, PDBj:5h6r
PDBsum	5h6r
PubMed	28336409
UniProt	O60341\|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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