5CVD

Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5cvda1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	AD-003 protein-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5cvda2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5cvdb1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	AD-003 protein-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5cvdb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8040269	3000118	SCOP2B (2022-06-29)
B	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)
A	Methyltransf_11_3	e5cvdA1	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)
B	Methyltransf_11_3	e5cvdB1	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)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	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
C [auth D], D [auth E]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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	organonitrogen compound metabolic process protein methylation N-terminal protein amino acid methylation primary metabolic process macromolecule methylation protein alkylation N-terminal peptidyl-proline dimethylation organic substance metabolic process N-terminal peptidyl-proline methylation methylation N-terminal protein amino acid modification macromolecule modification peptidyl-amino acid modification peptidyl-proline modification organonitrogen compound metabolic process protein methylation N-terminal protein amino acid methylation primary metabolic process macromolecule methylation protein alkylation N-terminal peptidyl-proline dimethylation organic substance metabolic process N-terminal peptidyl-proline methylation methylation N-terminal protein amino acid modification macromolecule modification peptidyl-amino acid modification peptidyl-proline modification metabolic process protein metabolic process macromolecule metabolic process protein modification process cellular 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
C [auth D], D [auth E]	N-teminal peptide from Histone H3-like centromeric protein A	DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization chromosome organization protein-DNA complex assembly CENP-A containing chromatin assembly cellular component organization cellular component biogenesis protein-DNA complex organization organelle organization cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis protein-containing complex organization chromosome organization protein-DNA complex assembly CENP-A containing chromatin assembly cellular component organization cellular component biogenesis protein-DNA complex organization organelle organization cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis centromere complex assembly chromatin remodeling at centromere establishment of organelle localization cellular localization microtubule cytoskeleton organization spindle localization establishment or maintenance of cell polarity mitotic cell cycle localization establishment of mitotic spindle localization establishment of spindle localization establishment of spindle orientation organelle localization establishment of localization in cell cell cycle microtubule cytoskeleton organization involved in mitosis cell cycle process establishment of localization establishment of cell polarity mitotic cell cycle process establishment of mitotic spindle orientation microtubule-based process cytoskeleton organization cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis cell division organelle assembly non-membrane-bounded organelle assembly kinetochore assembly kinetochore organization protein localization protein localization to chromosome, centromeric region protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to chromatin protein localization to CENP-A containing chromatin	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol intracellular organelle organelle intracellular non-membrane-bounded organelle chromosome, centromeric region chromosome chromosomal region non-membrane-bounded organelle condensed chromosome, centromeric region condensed chromosome protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol intracellular organelle organelle intracellular non-membrane-bounded organelle chromosome, centromeric region chromosome chromosomal region non-membrane-bounded organelle condensed chromosome, centromeric region condensed chromosome protein-containing complex CENP-A containing chromatin protein-DNA complex nucleosome chromatin chromosome, centromeric core domain CENP-A containing nucleosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen pericentric heterochromatin heterochromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR008576	Alpha-N-methyltransferase NTM1	Family
C [auth D], D [auth E]	IPR009072	Histone-fold	Homologous Superfamily
C [auth D], D [auth E]	IPR007125	Histone H2A/H2B/H3	Domain
C [auth D], D [auth E]	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9BV86	ovarian cancer Sjogren syndrome
C [auth D], D [auth E]	Pharos: P49450	medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis adrenal cortex carcinoma breast cancer endometriosis hypertensive disorder large cell medulloblastoma malignant colon neoplasm malignant mesothelioma nasopharyngeal carcinoma ovarian cancer primitive neuroectodermal tumor atopic eczema medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis adrenal cortex carcinoma breast cancer endometriosis hypertensive disorder large cell medulloblastoma malignant colon neoplasm malignant mesothelioma nasopharyngeal carcinoma ovarian cancer primitive neuroectodermal tumor atopic eczema breast carcinoma glioblastoma IgA glomerulonephritis lung adenocarcinoma malignant ependymoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma psoriasis atypical teratoid rhabdoid tumor ductal breast carcinoma in situ hepatocellular carcinoma invasive ductal breast carcinoma lung cancer malignant glioma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth D], D [auth E]	DMG	RESID: AA0620 PSI-MOD : N,N-dimethylglycine MOD:01983

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.