7XE3 | pdb_00007xe3

Crystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024)

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SWIRM	e7xe3A5	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: SWIRM	ECOD (1.6)
A	Amino_oxidase_2nd	e7xe3A1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: Amino_oxidase_2nd	ECOD (1.6)
A	Amino_oxidase_1st	e7xe3A4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Amino_oxidase_1st	ECOD (1.6)
A	zf-CW	e7xe3A3	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: zf-CW	ECOD (1.6)
A	zf-C3HC4_4	e7xe3A2	A: few secondary structure elements	X: C4H2C2-type zinc finger (From Topology)	H: C4H2C2-type zinc finger (From Topology)	T: C4H2C2-type zinc finger	F: zf-C3HC4_4	ECOD (1.6)
B	SWIRM	e7xe3B1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: SWIRM	ECOD (1.6)
B	Amino_oxidase_2nd	e7xe3B3	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: Amino_oxidase_2nd	ECOD (1.6)
B	Amino_oxidase_1st	e7xe3B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Amino_oxidase_1st	ECOD (1.6)
B	zf-CW	e7xe3B4	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: zf-CW	ECOD (1.6)
B	zf-C3HC4_4	e7xe3B5	A: few secondary structure elements	X: C4H2C2-type zinc finger (From Topology)	H: C4H2C2-type zinc finger (From Topology)	T: C4H2C2-type zinc finger	F: zf-C3HC4_4	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07496	CW-type Zinc Finger (zf-CW)	CW-type Zinc Finger	This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by [1], and is predicted to be a "highly specialised mononuclear four-cysteine zinc finger...that plays ...	This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by [1], and is predicted to be a "highly specialised mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including ...chromatin methylation status and early embryonic development." Weak homology to Pfam:PF00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteristic of vertebrates, higher plants and other animals in which these domain is found [1].	Domain
A, B	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
A, B	PF01593	Flavin containing amine oxidoreductase (Amino_oxidase)	Flavin containing amine oxidoreductase	This family consists of various amine oxidases, including maze polyamine oxidase (PAO) [1] and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene ...	This family consists of various amine oxidases, including maze polyamine oxidase (PAO) [1] and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role regulating the intracellular levels of amines via there oxidation; these include various neurotransmitters, neurotoxins and trace amines [2]. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium [3]. PAOs in plants, bacteria and protozoa oxidase spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines [1]. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Lysine-specific histone demethylase 1B	oxidoreductase activity catalytic activity protein binding binding histone binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding catalytic activity, acting on a protein oxidoreductase activity catalytic activity protein binding binding histone binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding catalytic activity, acting on a protein protein demethylase activity histone modifying activity histone demethylase activity demethylase activity FAD-dependent H3K4me/H3K4me3 demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone H3 demethylase activity histone H3K4 demethylase activity cation binding transition metal ion binding zinc ion binding metal ion binding	regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process sexual reproduction cellular developmental process reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation cell differentiation anatomical structure development developmental process epigenetic programming of gene expression multicellular organismal reproductive process genomic imprinting germ cell development epigenetic programming in the zygotic pronuclei epigenetic programing of female pronucleus	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus membrane-enclosed lumen protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B	IPR002937	Amine oxidase	Domain
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR050281	Flavin monoamine oxidase and related enzymes	Family
A, B	IPR007526	SWIRM domain	Domain
A, B	IPR011124	Zinc finger, CW-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q8NB78	atrial fibrillation adenoma breast cancer large cell medulloblastoma osteosarcoma glioblastoma medulloblastoma tuberculosis atypical teratoid rhabdoid tumor juvenile dermatomyositis myopathy

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.