Structure of PDB 7xe2 Chain B

Receptor sequence

>7xe2B (length=741) Species: 9606 (Homo sapiens) [Search protein sequence]

KYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDH
YYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECR
KWRQLTKEIQLTPQIAKTYRCGMKSDHCSLPEDLRVLEVSNHWWYSMLIL
PPLLKDSVAAPLLSAYYPDCVGMSPSCTSTNRGMNRYFQPFYQPNECGKA
LCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKC
IPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYH
NKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVT
VGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDK
RMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSEL
EGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSV
IIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLAL
LQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFF
GHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQ
QCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDI
IAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

3D structure

PDB

7xe2 Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2

Chain

Resolution

2.05 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	B	C142 C147 C169 C185	C94 C99 C121 C128
BS02	ZN	B	C53 C58 H84 H90	C5 C10 H36 H42
BS03	ZN	B	C65 C73 C95	C17 C25 C47
BS04	FAD	B	I388 G389 G391 P392 A393 E412 A413 K414 G419 R420 G435 A436 I438 V598 V627 P628 I637 W757 W762 I763 A766 G794 E795 Q803 T804 V805 A808	I307 G308 G310 P311 A312 E331 A332 K333 G338 R339 G354 A355 I357 V517 V546 P547 I556 W676 W681 I682 A685 G713 E714 Q722 T723 V724 A727
BS05	DIJ	B	I438 N440 Y545 Y767	I357 N359 Y464 Y686
BS06	FAD	B	I388 G389 G391 P392 A393 E412 A413 K414 G419 R420 G435 A436 Q437 I438 P597 V598 V627 P628 I637 I659 W757 W762 I763 A766 Y767 G794 E795 Q803 T804 V805 A808	I307 G308 G310 P311 A312 E331 A332 K333 G338 R339 G354 A355 Q356 I357 P516 V517 V546 P547 I556 I578 W676 W681 I682 A685 Y686 G713 E714 Q722 T723 V724 A727
BS07	DIJ	B	N440 Y767 T804	N359 Y686 T723

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

View graph for
Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:7xe2, PDBe:7xe2, PDBj:7xe2
PDBsum	7xe2
PubMed
UniProt	Q8NB78\|KDM1B_HUMAN Lysine-specific histone demethylase 2 (Gene Name=KDM1B)

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