3DAL | pdb_00003dal

Methyltransferase domain of human PR domain-containing protein 1

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)
B	SCOP2B Superfamily	SET domain	8088213	3000162	SCOP2B (2022-06-29)
A	SCOP2 Family	Histone lysine methyltransferases	8088212	4000376	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SET domain	8088213	3000162	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Ras	e3dalB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Ras	ECOD (develop294)
A	Resolvase	e3dalA1	A: alpha bundles	X: Profilin-like	H: sensor domains	T: sensor domains	F: Resolvase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)
A	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21549	PR domain zinc finger protein 2, PR domain (PRDM2_PR)	PR domain zinc finger protein 2, PR domain	This domain is found in PR domain zinc protein 2 from humans (PRDM2) and similar proteins from animals. PRDM2 is a histone methyltransferase that functions as a DNA-binding transcription factor. It contains a PR (PRDI-BF1 and RIZ1 homology) domain, w ...	This domain is found in PR domain zinc protein 2 from humans (PRDM2) and similar proteins from animals. PRDM2 is a histone methyltransferase that functions as a DNA-binding transcription factor. It contains a PR (PRDI-BF1 and RIZ1 homology) domain, which is a distinct SET domain, that is responsible for its catalytic activity (this entry). This domain displays a typical SET fold consisting mainly of short beta-strands and intervening loops including a pseudo-knot at the C terminus [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PR domain zinc finger protein 1	DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding promoter-specific chromatin binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity histone methyltransferase binding protein binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	sebum secreting cell proliferation cell population proliferation cellular process epithelial cell proliferation developmental process heart development multicellular organismal process animal organ development ventricular septum development circulatory system development multicellular organism development cardiac septum development cardiac chamber development anatomical structure development sebum secreting cell proliferation cell population proliferation cellular process epithelial cell proliferation developmental process heart development multicellular organismal process animal organ development ventricular septum development circulatory system development multicellular organism development cardiac septum development cardiac chamber development anatomical structure development cardiac ventricle development system development response to stimulus immune response immune system process adaptive immune response regulation of leukocyte differentiation regulation of cellular process cellular developmental process regulation of developmental process regulation of leukocyte activation cell development regulation of cell activation mononuclear cell differentiation regulation of cell differentiation lymphocyte activation lymphocyte differentiation regulation of cell development extrathymic T cell differentiation leukocyte activation regulation of T cell differentiation T cell activation cell differentiation T cell differentiation regulation of immune system process regulation of multicellular organismal process regulation of lymphocyte differentiation regulation of biological process regulation of multicellular organismal development hemopoiesis cell activation biological regulation regulation of T cell activation regulation of hemopoiesis regulation of extrathymic T cell differentiation leukocyte differentiation regulation of lymphocyte activation sexual reproduction reproductive process multicellular organismal reproductive process cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation germ cell development regulation of biosynthetic process positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process methylation biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism response to stress innate immune response response to external biotic stimulus regulation of natural killer cell differentiation regulation of natural killer cell activation natural killer cell differentiation natural killer cell activation anatomical structure morphogenesis morphogenesis of a branching structure sensory organ development retina development in camera-type eye visual system development neural retina development neurogenesis eye morphogenesis neuron differentiation animal organ morphogenesis sensory system development camera-type eye morphogenesis eye development nervous system development retinal bipolar neuron differentiation glutamatergic neuron differentiation generation of neurons retina morphogenesis in camera-type eye sensory organ morphogenesis camera-type eye development artery development aorta development vasculature development blood vessel development blood vessel morphogenesis tube development tube morphogenesis artery morphogenesis photoreceptor cell differentiation eye photoreceptor cell differentiation photoreceptor cell development eye photoreceptor cell development neuron development cell differentiation involved in embryonic placenta development placenta development chordate embryonic development embryo development in utero embryonic development trophoblast giant cell differentiation embryonic placenta development embryo development ending in birth or egg hatching embryonic organ development multi-multicellular organism process maternal process involved in female pregnancy maternal placenta development female pregnancy multi-organism reproductive process heart valve development regulation of alpha-beta T cell activation regulation of alpha-beta T cell differentiation alpha-beta T cell differentiation alpha-beta T cell activation NK T cell differentiation regulation of NK T cell differentiation cell fate commitment epithelium development digestive system development intestinal epithelial cell differentiation intestinal epithelial cell development tissue development digestive tract development epithelial cell differentiation epithelial cell development columnar/cuboidal epithelial cell development columnar/cuboidal epithelial cell differentiation regulation of cell population proliferation RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of biological process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process coronary vasculature development kidney development renal system development post-embryonic development	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR046341	SET domain superfamily	Homologous Superfamily
A, B	IPR050331	Zinc finger PRDM4/PRDM1/PRDM14-like	Family
A, B	IPR013087	Zinc finger C2H2-type	Domain
A, B	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A, B	IPR044413	PRDM1, PR/SET domain	Domain
A, B	IPR001214	SET domain	Domain
A, B	IPR016608	PR domain zinc finger protein 1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O75626	ulcerative colitis rheumatoid arthritis Sjogren syndrome systemic lupus erythematosus pancreatic ductal adenocarcinoma primary biliary cholangitis Sicca Syndrome spina bifida acne cystic fibrosis gastric cancer inflammatory bowel disease lung carcinoma malignant pancreatic neoplasm osteosarcoma ulcerative colitis rheumatoid arthritis Sjogren syndrome systemic lupus erythematosus pancreatic ductal adenocarcinoma primary biliary cholangitis Sicca Syndrome spina bifida acne cystic fibrosis gastric cancer inflammatory bowel disease lung carcinoma malignant pancreatic neoplasm osteosarcoma pilocytic astrocytoma psoriasis acute myeloid leukemia diffuse large B-cell lymphoma gastric carcinoma invasive ductal breast carcinoma MALT lymphoma ovarian cancer plasma cell myeloma systemic sclerosis Crohn disease exocrine pancreatic carcinoma glioblastoma malignant glioma myositis

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.