Structure of PDB 7xe3 Chain A

Receptor sequence

>7xe3A (length=747) Species: 9606 (Homo sapiens) [Search protein sequence]

SEKKYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNEC
FDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKP
ECRKWRQLTKEIQLTPQIAKTYRCGMKPNTTSDHCSLPEDLRVLEVSNHW
WYSMLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTSVPGMNRYFQPFYQP
NECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEA
LTPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYL
LPKDYHNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDK
SFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRIT
DPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESG
IQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLL
TPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLV
TVPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKV
QGADFFGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLD
DKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGS
GEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

3D structure

PDB

7xe3 Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2

Chain

Resolution

2.82 Å

3D
structure

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Enzymatic activity

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)
BS01	ZN	A	C142 C147 C169 C185	C97 C102 C124 C135
BS02	ZN	A	C53 C58 H84 H90	C8 C13 H39 H45
BS03	ZN	A	C65 C73 C95	C20 C28 C50
BS04	FAD	A	I388 G389 G391 P392 A393 E412 A413 G419 R420 G435 A436 I438 V598 V627 P628 I637 W757 W762 A766 Y767 G794 E795 Q803 T804 V805 A808	I313 G314 G316 P317 A318 E337 A338 G344 R345 G360 A361 I363 V523 V552 P553 I562 W682 W687 A691 Y692 G719 E720 Q728 T729 V730 A733
BS05	8A2	A	N440 Y767 Q803 T804	N365 Y692 Q728 T729

Gene Ontology

	Molecular Function
GO:0003682	chromatin binding
GO:0005515	protein binding
GO:0008270	zinc ion binding
GO:0016491	oxidoreductase activity
GO:0032452	histone demethylase activity
GO:0032453	histone H3K4 demethylase activity
GO:0042393	histone binding
GO:0046872	metal ion binding
GO:0050660	flavin adenine dinucleotide binding
GO:0071949	FAD binding
GO:0140682	FAD-dependent H3K4me/H3K4me3 demethylase activity

	Biological Process
GO:0006325	chromatin organization
GO:0006338	chromatin remodeling
GO:0044726	epigenetic programing of female pronucleus
GO:0071514	genomic imprinting

	Cellular Component
GO:0000786	nucleosome
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005694	chromosome

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:7xe3, PDBe:7xe3, PDBj:7xe3
PDBsum	7xe3
PubMed
UniProt	Q8NB78\|KDM1B_HUMAN Lysine-specific histone demethylase 2 (Gene Name=KDM1B)

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