Structure of PDB 7xe1 Chain B

Receptor sequence

>7xe1B (length=740) Species: 9606 (Homo sapiens) [Search protein sequence]

KKYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFD
HYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPEC
RKWRQLTKEIQLTPQIAKTYRCGMKPSDHCSLPEDLRVLEVSNHWWYSML
ILPPLLKDSVAAPLLSAYYPDCVGMSPSCTPGMNRYFQPFYQPNECGKAL
CVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCI
PHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHN
KSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTV
GRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDKR
MDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELE
GQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVI
IEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALL
QKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFG
HVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQ
CMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDII
AEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

3D structure

PDB

7xe1 Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2

Chain

Resolution

2.07 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	C95 C100 C122 C130
BS02	ZN	B	C53 C58 H84 H90	C6 C11 H37 H43
BS03	ZN	B	C65 C73 C95	C18 C26 C48
BS04	FAD	B	I388 G389 G391 P392 A393 E412 A413 K414 G419 R420 G435 A436 Q437 I438 V598 V627 P628 I659 W757 W762 A766 G794 E795 Q803 T804 V805 A808	I306 G307 G309 P310 A311 E330 A331 K332 G337 R338 G353 A354 Q355 I356 V516 V545 P546 I577 W675 W680 A684 G712 E713 Q721 T722 V723 A726
BS05	DIJ	B	N440 K661 T804	N358 K579 T722

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:7xe1, PDBe:7xe1, PDBj:7xe1
PDBsum	7xe1
PubMed
UniProt	Q8NB78\|KDM1B_HUMAN Lysine-specific histone demethylase 2 (Gene Name=KDM1B)

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