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	Ion_trans	e6kdrB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Ion_trans	ECOD (v294.1)
A	Ion_trans	e6kdrA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Ion_trans	ECOD (v294.1)

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.