6KDR | pdb_00006kdr

Crystal structure of human NRMT2 in complex with human centromere protein B peptide

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	S-adenosyl-L-methionine-dependent methyltransferases	8085520	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8085520	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	e6kdrB1	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	e6kdrA1	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 (utative)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)

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]	Peptide from Major centromere autoantigen B	DNA binding binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding satellite DNA binding centromeric DNA binding chromatin binding	-	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, centromeric region chromosomal region condensed chromosome, centromeric region condensed chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, centromeric region chromosomal region condensed chromosome, centromeric region condensed chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen pericentric heterochromatin chromatin heterochromatin
A, B	Alpha N-terminal protein methyltransferase 1B	N-terminal protein N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity	protein methylation N-terminal protein amino acid methylation primary metabolic process macromolecule methylation protein alkylation methylation N-terminal protein amino acid modification macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D], D [auth E]	IPR009057	Homedomain-like superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR015115	Centromere protein CENP-B, C-terminal domain	Domain
C [auth D], D [auth E]	IPR004875	DDE superfamily endonuclease domain	Domain
C [auth D], D [auth E]	IPR034882	CENP-B, dimerisation domain superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR006600	HTH CenpB-type DNA-binding domain	Domain
C [auth D], D [auth E]	IPR007889	DNA binding HTH domain, Psq-type	Domain
C [auth D], D [auth E]	IPR050863	Centromere and Transposable Element-Derived Protein	Family
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
C [auth D], D [auth E]	Pharos: P07199	atypical teratoid rhabdoid tumor malignant glioma glioblastoma malignant mesothelioma large cell medulloblastoma osteosarcoma

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.