Structure of PDB 4gu0 Chain B Binding Site BS01

Receptor Information
>4gu0 Chain B (length=748) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLGSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECF
DHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPE
CRKWRQLTKEIQLTPQIAKTYRCGMKPNTAIKPETSDHCSLPEDLRVLEV
SNHWWYSMLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTGMNRYFQPFYQ
PNECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKE
ALTPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQY
LLPKDYHNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDD
KSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRI
TDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKES
GIQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTL
LTPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVL
VTVPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSK
VQGADFFGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTL
DDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGG
SGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF
Ligand information
>4gu0 Chain F (length=26) Species: 9606 (Homo sapiens) [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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PDB4gu0 Structural insight into substrate recognition by histone demethylase LSD2/KDM1b
Resolution3.103 Å
Binding residue
(original residue number in PDB)		S221 A222 Y223 Y224 C227 Y273 N276 E277 D287 N440 F461 C465 L467 D480 N488 D492 S495 N542 W559 N562 E563 Q567 H572 F680 Q803
Binding residue
(residue number reindexed from 1)		S175 A176 Y177 Y178 C181 Y199 N202 E203 D213 N366 F387 C391 L393 D406 N414 D418 S421 N468 W485 N488 E489 Q493 H498 F606 Q729
Enzymatic activity
Catalytic site (original residue number in PDB) N440
Catalytic site (residue number reindexed from 1) N366
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:4gu0, PDBe:4gu0, PDBj:4gu0
PDBsum4gu0
PubMed23357850
UniProtQ8NB78|KDM1B_HUMAN Lysine-specific histone demethylase 2 (Gene Name=KDM1B)

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