Structure of PDB 7xe3 Chain B

Receptor sequence

>7xe3B (length=742) Species: 9606 (Homo sapiens) [Search protein sequence]

KYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDH
YYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECR
KWRQLTKEIQLTPQIAKTYRCGMKPSDHCSLPEDLRVLEVSNHWWYSMLI
LPPLLKDSVAAPLLSAYYPDCVGMSPSCTSTNRGMNRYFQPFYQPNECGK
ALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQK
CIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDY
HNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGV
TVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTID
KRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSE
LEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYS
VIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLA
LLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADF
FGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVL
QQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYD
IIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

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

[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

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 C129
BS02	ZN	B	C58 H84 H90	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 Q437 I438 P597 V598 V627 P628 I637 W757 W762 I763 A766 G794 E795 Q803 T804 V805 A808	I308 G309 G311 P312 A313 E332 A333 K334 G339 R340 G355 A356 Q357 I358 P517 V518 V547 P548 I557 W677 W682 I683 A686 G714 E715 Q723 T724 V725 A728
BS05	8A2	B	N440 Y767 Q803 T804	N360 Y687 Q723 T724

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

View graph for
Biological Process

View graph for
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)

[Back to BioLiP]