1P0Y | pdb_00001p0y

Crystal structure of the SET domain of LSMT bound to MeLysine and AdoHcy

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d1p0yc1	All alpha proteins	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	pea (Lathyrus oleraceus ) [TaxId: 3888 ],	SCOPe (2.08)
C	d1p0yc2	All beta proteins	beta-clip	SET domain	RuBisCo LSMT catalytic domain	RuBisCo LSMT catalytic domain	pea (Lathyrus oleraceus ) [TaxId: 3888 ],	SCOPe (2.08)
C	d1p0yc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	pea (Lathyrus oleraceus ) [TaxId: 3888 ],	SCOPe (2.08)
B	d1p0yb1	All alpha proteins	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	pea (Lathyrus oleraceus ) [TaxId: 3888 ],	SCOPe (2.08)
B	d1p0yb2	All beta proteins	beta-clip	SET domain	RuBisCo LSMT catalytic domain	RuBisCo LSMT catalytic domain	pea (Lathyrus oleraceus ) [TaxId: 3888 ],	SCOPe (2.08)
B	d1p0yb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	pea (Lathyrus oleraceus ) [TaxId: 3888 ],	SCOPe (2.08)
A	d1p0ya1	All alpha proteins	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	pea (Lathyrus oleraceus ) [TaxId: 3888 ],	SCOPe (2.08)
A	d1p0ya2	All beta proteins	beta-clip	SET domain	RuBisCo LSMT catalytic domain	RuBisCo LSMT catalytic domain	pea (Lathyrus oleraceus ) [TaxId: 3888 ],	SCOPe (2.08)
A	d1p0ya3	Artifacts	Tags	Tags	Tags	C-terminal Tags	pea (Lathyrus oleraceus ) [TaxId: 3888 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	SET domain	8042118	3000162	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RuBisCo LSMT C-terminal, substrate-binding domain	8042117	3001192	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SET domain	8042118	3000162	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RuBisCo LSMT C-terminal, substrate-binding domain	8042117	3001192	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RuBisCo LSMT C-terminal, substrate-binding domain	8042117	3001192	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SET domain	8042118	3000162	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)
C	Autotransporter	e1p0yC1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Autotransporter	ECOD (v294.1)
C		e1p0yC2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F:	ECOD (v294.1)
B	Autotransporter	e1p0yB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Autotransporter	ECOD (v294.1)
B		e1p0yB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F:	ECOD (v294.1)
A	Autotransporter	e1p0yA1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Autotransporter	ECOD (v294.1)
A		e1p0yA2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.90.1410.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 1	set domain protein methyltransferase, domain 1	CATH (4.3.0)
C	3.90.1420.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 2	Rubisco LSMT, substrate-binding domain	CATH (4.3.0)
B	3.90.1410.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 1	set domain protein methyltransferase, domain 1	CATH (4.3.0)
B	3.90.1420.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 2	Rubisco LSMT, substrate-binding domain	CATH (4.3.0)
A	3.90.1410.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 1	set domain protein methyltransferase, domain 1	CATH (4.3.0)
A	3.90.1420.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 2	Rubisco LSMT, substrate-binding domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast	protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity	methylation metabolic process cellular process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR050600	SETD3/SETD6 methyltransferase	Family
A, B, C	IPR036464	Rubisco LSMT, substrate-binding domain superfamily	Homologous Superfamily
A, B, C	IPR046341	SET domain superfamily	Homologous Superfamily
A, B, C	IPR011192	Rubisco LSMT methyltransferase, plant	Family
A, B, C	IPR015353	Rubisco LSMT, substrate-binding domain	Domain
A, B, C	IPR001214	SET domain	Domain
A, B, C	IPR044431	RBCMT, SET domain	Domain

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.