6NM4 | pdb_00006nm4

Crystal structure of SAM-bound PRDM9 in complex with MRK-740 inhibitor

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	SET domain	8054027	3000162	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SET domain	8054027	3000162	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)
B	SET_4	e6nm4B1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET_4	ECOD (1.6)
A	SET_4	e6nm4A1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET_4	ECOD (1.6)

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 (utative)
A	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (utative)

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	Histone-lysine N-methyltransferase PRDM9	protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups histone H3K9 methyltransferase activity transferase activity histone H3K9 trimethyltransferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups histone H3K9 methyltransferase activity transferase activity histone H3K9 trimethyltransferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding recombination hotspot binding histone H3K4 methyltransferase activity histone H3K4 trimethyltransferase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity histone H3K36 methyltransferase activity histone H3K36 trimethyltransferase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding histone H4 methyltransferase activity histone H4K20 methyltransferase activity histone H4K20 monomethyltransferase activity histone H4K20me methyltransferase activity	regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death methylation regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death methylation metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process sexual reproduction reproductive process multicellular organismal reproductive process male gamete generation gamete generation meiotic chromosome segregation meiotic cell cycle organelle fission chromosome organization meiotic cell cycle process cellular component organization chromosome organization involved in meiotic cell cycle nuclear division organelle organization meiosis I meiosis I cell cycle process homologous chromosome pairing at meiosis nuclear chromosome segregation meiotic nuclear division homologous chromosome segregation cell cycle cellular component organization or biogenesis chromosome segregation cell cycle process homologous recombination DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process meiotic gene conversion nucleobase-containing compound metabolic process gene conversion female gamete generation RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription regulation of reproductive process fertilization positive regulation of biological process regulation of fertilization positive regulation of fertilization positive regulation of reproductive process cellular response to stimulus response to stimulus cellular response to stress response to stress reciprocal homologous recombination DNA repair double-strand break repair reciprocal meiotic recombination DNA damage response double-strand break repair involved in meiotic recombination positive regulation of organelle organization positive regulation of reciprocal meiotic recombination regulation of DNA recombination positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of DNA recombination regulation of meiotic cell cycle regulation of cell cycle process positive regulation of nuclear division regulation of organelle organization positive regulation of DNA metabolic process positive regulation of meiotic nuclear division regulation of DNA metabolic process regulation of cellular component organization positive regulation of cellular component organization regulation of reciprocal meiotic recombination positive regulation of cell cycle process regulation of cell cycle positive regulation of cellular process positive regulation of meiotic cell cycle positive regulation of cell cycle regulation of meiotic nuclear division regulation of nuclear division	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001909	Krueppel-associated box	Domain
A, B	IPR046341	SET domain superfamily	Homologous Superfamily
A, B	IPR013087	Zinc finger C2H2-type	Domain
A, B	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A, B	IPR044417	PRDM7/PRDM9, PR/SET domain	Domain
A, B	IPR001214	SET domain	Domain
A, B	IPR003655	Ancestral KRAB domain	Domain
A, B	IPR019041	SSXRD motif	Conserved Site
A, B	IPR036051	Krueppel-associated box domain superfamily	Homologous Superfamily
A, B	IPR048414	Histone-lysine N-methyltransferase PRDM9-like, C2H2 zinc finger-like	Domain

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.