Het-PDB Navi2 (PDB: 4GUU)

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Ligands
Code	Name		Style	Show	Link
FA9	[(2r,3s,4r,5r)-5-(6-amino-9h-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2r,3s,4s)-5-[(3r,3as,7ar)-10,11-dimethyl-1,4,6-trioxo-3-phenyl-2,3,5,6,7,7a-hexahydro-1h-benzo[G]pyrrolo[2,1-E]pteridin-8(4h)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate				PoSSuM
ZN	Zinc ion				PoSSuM

Non-standard Residues
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Glycosylation
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Download interaction data: 4GUU

Code :

4GUU PDBj RCSB PDB PDBe

Header :

OXIDOREDUCTASE

Title :

Crystal structure of LSD2-NPAC with tranylcypromine

Release Data :

2013-01-16

Compound :

mol_id	molecule	chains	synonym
1	Lysine-specific histone demethylase 1B	A	LSD2, Flavin-containing amine oxidase domain-containing protein 1, Lysine-specific histone demethylase 2
	ec: 1.-.-.- fragment: UNP residues 51-822

mol_id	molecule	chains	synonym
2	Putative oxidoreductase GLYR1	B	NPAC, 3-hydroxyisobutyrate dehydrogenase-like protein, Cytokine-like nuclear factor N-PAC, Glyoxylate reductase 1 homolog, Nuclear protein NP60, Nuclear protein of 60 kDa
	ec: 1.-.-.- fragment: UNP residues 152-268

Source :

mol_id	organism_scientific	organism_common	expression_system
1	Homo sapiens (taxid:9606)	Human	Spodoptera frugiperda (taxid:7108)
	gene: LSD2 expression_system_common: Fall armyworm expression_system_cell_line: sf9 expression_system_vector_type: Baculovirus expression_system_plasmid: pFastBac1

mol_id	organism_scientific	organism_common	expression_system
2	Homo sapiens (taxid:9606)	Human	Escherichia coli (taxid:562)
	gene: GLYR1

Authors :

Chen, F., Dong, Z., Fang, J., Yang, Y., Li, Z., Xu, Y., Yang, H., Wang, P., Xu, Y.

Keywords :

histone demethylase, OXIDOREDUCTASE

Exp. method :

X-RAY DIFFRACTION ( 2.302 Å )

Citation :

LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation

Fang, R.,Chen, F.,Dong, Z. et al.
(2013) Mol.Cell 49 : 558 - 570

Chain :

UniProt :

Q8NB78 (KDM1B_HUMAN)

Reaction:	EC:	Evidence:
Reaction:	Physiological Direction:	Evidence:
2 A + 2 H2O + N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] = 2 AH2 + 2 formaldehyde + L-lysyl(4)-[histone H3]	1.14.99.66	PubMed:23260659, PubMed:23357850, PubMed:30970244
	left-to-right	PubMed:30970244
A + H2O + N(6)-methyl-L-lysyl(4)-[histone H3] = AH2 + formaldehyde + L-lysyl(4)-[histone H3]	-	PubMed:30970244
	left-to-right	PubMed:30970244

PDB ID: 4GUU