Structure of PDB 6r25 Chain K

Receptor sequence

>6r25K (length=737) Species: 9606 (Homo sapiens) [Search protein sequence]

GSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDH
YYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECR
KWRQLTKEIQLTPQIAKTYRCGMKSDHCSLPEDLRVLEVSNHWWYSMLIL
PPLLKDSVAAPLLSAYYPDCVGMSPSCTGMNRYFQPFYQPNECGKALCVR
PDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHI
IVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSV
IIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRG
AQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDF
HFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELEGQV
LQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEK
LAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKG
AIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVP
PSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMA
TLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAED
IQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

3D structure

PDB

6r25 A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.

Chain

Resolution

4.61 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	N440
Catalytic site (residue number reindexed from 1)	N355
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	peptide	K	Y273 G279 L282 C283 V284 E290 D292 K359 L361 A566 N798 H800 F801 R814	Y188 G194 L197 C198 V199 E205 D207 K274 L276 A481 N713 H715 F716 R729
BS02	peptide	K	A222 Y223 Y224 P225 P275 N276 E277 C278 R285 D287 N440 C465 L467 D480 N488 L491 D492 S495 N542 A546 W559 N562 E563 H572 F680 Q803	A165 Y166 Y167 P168 P190 N191 E192 C193 R200 D202 N355 C380 L382 D395 N403 L406 D407 S410 N457 A461 W474 N477 E478 H487 F595 Q718
BS03	dna	K	N276 C278	N191 C193
BS04	FAD	K	I388 G389 G391 P392 A393 E412 A413 K414 G419 R420 G435 A436 I438 V598 V627 P628 W757 W762 A766 Y767 E795 Q803 T804 V805 A808	I303 G304 G306 P307 A308 E327 A328 K329 G334 R335 G350 A351 I353 V513 V542 P543 W672 W677 A681 Y682 E710 Q718 T719 V720 A723
BS05	ZN	K	C53 C58 H84 H90	C5 C10 H36 H42
BS06	ZN	K	C65 C73 C95	C17 C25 C47
BS07	ZN	K	C142 C147 C169 C185	C94 C99 C121 C128

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:6r25, PDBe:6r25, PDBj:6r25
PDBsum	6r25
PubMed	30970244
UniProt	Q8NB78\|KDM1B_HUMAN Lysine-specific histone demethylase 2 (Gene Name=KDM1B)

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