2YDX | pdb_00002ydx

Crystal structure of human S-adenosylmethionine synthetase 2, beta subunit

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2ydxb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2ydxb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2ydxb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2ydxc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2ydxc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2ydxc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2ydxe1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2ydxe3	Artifacts	Tags	Tags	Tags	C-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2ydxe2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2ydxd1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2ydxd3	Artifacts	Tags	Tags	Tags	C-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2ydxd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2ydxa1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2ydxa3	Artifacts	Tags	Tags	Tags	C-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2ydxa2	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)
B	SCOP2B Superfamily	SDR-like	8088242	3000038	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SDR-like	8088242	3000038	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	SDR-like	8088242	3000038	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SDR-like	8088242	3000038	SCOP2B (2022-06-29)
A	SCOP2 Family	UDP-glucose 4-epimerase GalE-lke	8088241	4000088	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SDR-like	8088242	3000038	SCOP2 (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		e2ydxB1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Radical_SAM	F:	ECOD (20:10:01)
C		e2ydxC1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Radical_SAM	F:	ECOD (20:10:01)
E		e2ydxE1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Radical_SAM	F:	ECOD (20:10:01)
D		e2ydxD1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Radical_SAM	F:	ECOD (20:10:01)
A		e2ydxA1	A: Glucose permease domain IIB-like	X: eIF1-like	H: eIF1-like	T: Tautomerase, Tautomerase_2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF04321	RmlD substrate binding domain (RmlD_sub_bind)	RmlD substrate binding domain	L-rhamnose is a saccharide required for the virulence of some bacteria. Its precursor, dTDP-L-rhamnose, is synthesised by four different enzymes the final one of which is RmlD. The RmlD substrate binding domain is responsible for binding a sugar nucl ...	L-rhamnose is a saccharide required for the virulence of some bacteria. Its precursor, dTDP-L-rhamnose, is synthesised by four different enzymes the final one of which is RmlD. The RmlD substrate binding domain is responsible for binding a sugar nucleotide [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA	enzyme regulator activity molecular function regulator activity methionine adenosyltransferase regulator activity protein binding binding enzyme binding	sulfur compound biosynthetic process biosynthetic process S-adenosylmethionine biosynthetic process S-adenosylmethionine metabolic process sulfur compound metabolic process metabolic process cellular process small molecule metabolic process one-carbon metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex methionine adenosyltransferase complex transferase complex intracellular protein-containing complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex methionine adenosyltransferase complex transferase complex intracellular protein-containing complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR029903	RmlD-like, substrate binding domain	Domain
A, B, C, D, E	IPR005913	dTDP-4-dehydrorhamnose reductase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E	Pharos: Q9NZL9	attention deficit hyperactivity disorder, inattentive type ovarian cancer lung adenocarcinoma plasma cell myeloma multiple sclerosis Sjogren syndrome

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.