6E1F | pdb_00006e1f

Crystal structure of the SWIRM domain of human histone lysine-specific demethylase LSD1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Homeodomain-like	8001517	3000001	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Homeodomain-like	8001517	3000001	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Homeodomain-like	8001517	3000001	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Homeodomain-like	8001517	3000001	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e6e1fA1	A: Ten stranded beta/alpha barrel	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T:	F:	ECOD (20:10:01)
D		e6e1fD1	A: Ten stranded beta/alpha barrel	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Lsr2_DNA-bd (DEPRECATED)	F:	ECOD (20:10:01)
C		e6e1fC1	A: Ten stranded beta/alpha barrel	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Lsr2_DNA-bd (DEPRECATED)	F:	ECOD (20:10:01)
B		e6e1fB1	A: Ten stranded beta/alpha barrel	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Lsr2_DNA-bd (DEPRECATED)	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (utative)
D	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (utative)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (utative)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF04433	SWIRM domain (SWIRM)	SWIRM domain	This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Lysine-specific histone demethylase 1A	protein demethylase activity catalytic activity, acting on a protein catalytic activity demethylase activity transcription factor binding protein binding binding bHLH transcription factor binding DNA-binding transcription factor binding MRF binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding protein demethylase activity catalytic activity, acting on a protein catalytic activity demethylase activity transcription factor binding protein binding binding bHLH transcription factor binding DNA-binding transcription factor binding MRF binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding chromatin binding promoter-specific chromatin binding RNA binding telomeric repeat-containing RNA binding nucleic acid binding histone H4 demethylase activity histone H4K20 demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity dioxygenase activity oxidoreductase activity histone modifying activity 2-oxoglutarate-dependent dioxygenase activity histone H3 demethylase activity histone H3K4 demethylase activity FAD-dependent H3K4me/H3K4me3 demethylase activity identical protein binding p53 binding RNA polymerase II-specific DNA-binding transcription factor binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity nuclear receptor binding nuclear androgen receptor binding transcription corepressor activity histone H3K9 demethylase activity enzyme binding	nucleobase-containing compound metabolic process guanine metabolic process purine nucleobase metabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process purine-containing compound metabolic process cellular response to stimulus regulation of DNA recombination regulation of cellular process regulation of double-strand break repair nucleobase-containing compound metabolic process guanine metabolic process purine nucleobase metabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process purine-containing compound metabolic process cellular response to stimulus regulation of DNA recombination regulation of cellular process regulation of double-strand break repair response to stimulus regulation of cellular response to stress regulation of primary metabolic process cellular response to stress response to stress regulation of response to stress recombinational repair regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination DNA repair double-strand break repair regulation of biological process DNA recombination biological regulation DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination DNA damage response regulation of response to stimulus macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process DNA repair-dependent chromatin remodeling cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway regulation of signal transduction by p53 class mediator negative regulation of cellular process signal transduction intrinsic apoptotic signaling pathway negative regulation of signal transduction by p53 class mediator regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process signal transduction by p53 class mediator cell death negative regulation of signal transduction apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of cell communication intrinsic apoptotic signaling pathway by p53 class mediator apoptotic process regulation of intrinsic apoptotic signaling pathway by p53 class mediator programmed cell death regulation of apoptotic signaling pathway regulation of biosynthetic process epigenetic regulation of gene expression gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of stem cell proliferation cell population proliferation positive regulation of cell population proliferation positive regulation of biological process positive regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation positive regulation of cellular process regulation of neuron projection development multicellular organismal process regulation of cellular component organization positive regulation of cellular component organization cellular developmental process cell projection organization cell development neuron projection development neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development cell differentiation anatomical structure development positive regulation of cell projection organization system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization head development forebrain development animal organ development brain development pallium development cerebral cortex development central nervous system development telencephalon development muscle structure development muscle cell development muscle cell differentiation RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of neural precursor cell proliferation neural precursor cell proliferation regulation of neural precursor cell proliferation cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus response to ionizing radiation cellular response to gamma radiation response to radiation response to abiotic stimulus cellular response to abiotic stimulus response to gamma radiation regulation of epithelial to mesenchymal transition regulation of developmental process positive regulation of epithelial to mesenchymal transition regulation of cell differentiation mesenchyme development positive regulation of developmental process positive regulation of cell differentiation regulation of multicellular organismal process tissue development epithelial to mesenchymal transition positive regulation of multicellular organismal process mesenchymal cell differentiation developmental maturation anatomical structure maturation neuron maturation cell maturation DNA damage response, signal transduction by p53 class mediator negative regulation of DNA damage response, signal transduction by p53 class mediator regulation of DNA damage response, signal transduction by p53 class mediator signal transduction in response to DNA damage regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of protein modification process protein ubiquitination protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to nitrogen compound response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to cAMP homeostatic process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator response to light stimulus response to UV cellular response to light stimulus cellular response to UV regulation of localization localization regulation of protein localization macromolecule localization intracellular protein localization response to antibiotic response to fungicide response to toxic substance negative regulation of chromatin organization positive regulation of gene expression, epigenetic transcription initiation at RNA polymerase II promoter regulation of chromatin organization negative regulation of cellular component organization DNA-templated transcription initiation negative regulation of transcription initiation-coupled chromatin remodeling positive regulation of gene expression transcription initiation-coupled chromatin remodeling positive regulation of cell size regulation of cellular component size regulation of biological quality regulation of cell size regulation of anatomical structure size intracellular receptor signaling pathway response to lipid hormone-mediated signaling pathway cellular response to endogenous stimulus response to hormone response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway androgen receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus regulation of androgen receptor signaling pathway cellular response to lipid nuclear receptor-mediated signaling pathway neuroblast proliferation positive regulation of nervous system development regulation of neuroblast proliferation regulation of neurogenesis regulation of cell development regulation of nervous system development positive regulation of neurogenesis regulation of multicellular organismal development positive regulation of cell development positive regulation of neuroblast proliferation	protein-containing complex catalytic complex DNA repair complex membrane-bounded organelle histone methyltransferase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure protein-containing complex catalytic complex DNA repair complex membrane-bounded organelle histone methyltransferase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle methyltransferase complex nuclear lumen transcription regulator complex membraneless organelle intracellular membraneless organelle chromatin chromosome chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002937	Amine oxidase	Domain
A, B, C, D	IPR017366	Lysine-specific histone demethylase	Family
A, B, C, D	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR007526	SWIRM domain	Domain
A, B, C, D	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR050281	Flavin monoamine oxidase and related enzymes	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O60341	palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome hyperplasia Neoplasm Invasiveness malignant colon neoplasm non-small cell lung carcinoma benign colon neoplasm lung cancer cancer intellectual disability colonic neoplasm large cell medulloblastoma medulloblastoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.