Structure of PDB 6r25 Chain K Binding Site BS02

Receptor Information
>6r25 Chain K (length=737) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDH
YYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECR
KWRQLTKEIQLTPQIAKTYRCGMKSDHCSLPEDLRVLEVSNHWWYSMLIL
PPLLKDSVAAPLLSAYYPDCVGMSPSCTGMNRYFQPFYQPNECGKALCVR
PDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHI
IVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSV
IIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRG
AQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDF
HFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELEGQV
LQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEK
LAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKG
AIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVP
PSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMA
TLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAED
IQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF
Ligand information
>6r25 Chain M (length=26) Species: 8355 (Xenopus laevis) [Search peptide sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ARTMQTARKSTGGKAPRKQLATKAAR
Receptor-Ligand Complex Structure
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PDB6r25 A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.
Resolution4.61 Å
Binding residue
(original residue number in PDB)		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
Binding residue
(residue number reindexed from 1)		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
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.
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
PDBsum6r25
PubMed30970244
UniProtQ8NB78|KDM1B_HUMAN Lysine-specific histone demethylase 2 (Gene Name=KDM1B)

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