5CVE | pdb_00005cve

Crystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8040269	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8040269	3000118	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	Methyltransf_11_3	e5cveB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_3	ECOD (1.6)
A	Methyltransf_11_3	e5cveA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF05891	AdoMet dependent proline di-methyltransferase (Methyltransf_PK)	AdoMet dependent proline di-methyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], D [auth E]	N-terminal peptide from Histone H2B	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity protein-containing complex binding structural molecule activity structural constituent of chromatin	cellular component organization chromatin organization cellular process cellular component organization or biogenesis	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 intracellular membrane-bounded organelle
A, B	N-terminal Xaa-Pro-Lys N-methyltransferase 1	catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity histone modifying activity transferase activity methyltransferase activity catalytic activity histone methyltransferase activity N-terminal protein N-methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity	protein methylation N-terminal protein amino acid methylation primary metabolic process macromolecule methylation protein alkylation N-terminal peptidyl-proline dimethylation N-terminal peptidyl-proline methylation methylation N-terminal protein amino acid modification macromolecule modification peptidyl-amino acid modification peptidyl-proline modification metabolic process cellular process protein methylation N-terminal protein amino acid methylation primary metabolic process macromolecule methylation protein alkylation N-terminal peptidyl-proline dimethylation N-terminal peptidyl-proline methylation methylation N-terminal protein amino acid modification macromolecule modification peptidyl-amino acid modification peptidyl-proline modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process cell cycle chromosome segregation cell cycle process N-terminal peptidyl-serine trimethylation peptidyl-serine modification N-terminal peptidyl-serine methylation N-terminal peptidyl-glycine methylation peptidyl-glycine modification N-terminal peptidyl-serine dimethylation cellular component organization organelle organization microtubule cytoskeleton organization microtubule-based process cellular component organization or biogenesis cytoskeleton organization spindle organization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D], D [auth E]	IPR009072	Histone-fold	Homologous Superfamily
C [auth D], D [auth E]	IPR055333	Histone H2B, conserved site	Conserved Site
C [auth D], D [auth E]	IPR000558	Histone H2B	Family
C [auth D], D [auth E]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR008576	Alpha-N-methyltransferase NTM1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9BV86	ovarian cancer Sjogren syndrome

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth D], D [auth E]	PBE	RESID: AA0066 PSI-MOD : N,N-dimethyl-L-proline MOD:00075

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.