2RJF | pdb_00002rjf

Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 12-30), orthorhombic form I

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)
E	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037963	3000404	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037964	3000404	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037961	3000404	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037964	3000404	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037963	3000404	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037961	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037964	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037963	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8037961	3000404	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)
E	MBT	e2rjfE12	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MBT	ECOD (1.6)
C	MBT	e2rjfC12	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MBT	ECOD (1.6)
A	MBT	e2rjfA12	A: beta barrels	X: SH3	H: SH3	T: SH3	F: MBT	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF02820	mbt repeat (MBT)	mbt repeat	The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein Swiss:Q9VHA0. The repeat is found in up to four copies as in Swiss:Q9UHJ3. The repeat contains a completely conserved g ...	The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein Swiss:Q9VHA0. The repeat is found in up to four copies as in Swiss:Q9UHJ3. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	Lethal(3)malignant brain tumor-like protein	histone reader activity histone H4K20me2 reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding histone binding SAM domain binding protein domain specific binding chromatin binding cation binding transition metal ion binding histone reader activity histone H4K20me2 reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding histone binding SAM domain binding protein domain specific binding chromatin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding protein-containing complex binding nucleosome binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process developmental process cellular developmental process hemopoiesis cell differentiation anatomical structure development cell development multicellular organismal process regulation of developmental process regulation of megakaryocyte differentiation megakaryocyte differentiation regulation of cell differentiation regulation of cell development multicellular organism development regulation of immune system process regulation of multicellular organismal process regulation of multicellular organismal development regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression negative regulation of gene expression, epigenetic mitotic nuclear division regulation of cellular component organization regulation of cell cycle process organelle fission regulation of mitotic nuclear division regulation of organelle organization mitotic cell cycle regulation of mitotic cell cycle organelle organization nuclear division mitotic cell cycle process regulation of nuclear division cell cycle regulation of cell cycle cell cycle process constitutive heterochromatin formation	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome condensed chromosome membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle chromatin silencing complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome condensed chromosome membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle chromatin silencing complex chromatin lock complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen chromatin
B, D	Histone H4	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR036060	Zinc finger, C2H2C-type superfamily	Homologous Superfamily
A, C, E	IPR004092	Mbt repeat	Repeat
A, C, E	IPR002515	Zinc finger, C2H2C-type	Repeat
A, C, E	IPR047362	Lethal(3)malignant brain tumor-like protein 1, third MBT repeat	Repeat
A, C, E	IPR050548	Polycomb group and chromatin remodeling factors	Family
A, C, E	IPR047361	Lethal(3)malignant brain tumor-like protein 1, first MBT repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E	Pharos: Q9Y468	atypical teratoid rhabdoid tumor lung adenocarcinoma malignant glioma osteosarcoma glioblastoma lung cancer medulloblastoma ovarian cancer large cell medulloblastoma malignant ependymoma oligodendroglioma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

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.