3ROE | pdb_00003roe

Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymidine

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3roea_	Alpha and beta proteins (a/b)	YjeF N-terminal domain-like	YjeF N-terminal domain-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3roec_	Alpha and beta proteins (a/b)	YjeF N-terminal domain-like	YjeF N-terminal domain-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F	d3roef_	Alpha and beta proteins (a/b)	YjeF N-terminal domain-like	YjeF N-terminal domain-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d3roee_	Alpha and beta proteins (a/b)	YjeF N-terminal domain-like	YjeF N-terminal domain-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3roed_	Alpha and beta proteins (a/b)	YjeF N-terminal domain-like	YjeF N-terminal domain-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3roeb_	Alpha and beta proteins (a/b)	YjeF N-terminal domain-like	YjeF N-terminal domain-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	YjeF N-terminal domain-like	8080837	3000851	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YjeF N-terminal domain-like	8080837	3000851	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YjeF N-terminal domain-like	8080837	3000851	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	YjeF N-terminal domain-like	8080837	3000851	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	YjeF N-terminal domain-like	8080837	3000851	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YjeF N-terminal domain-like	8080837	3000851	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)
A		e3roeA1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: V-set	F:	ECOD (20:10:01)
C		e3roeC1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: V-set	F:	ECOD (20:10:01)
F		e3roeF1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: V-set	F:	ECOD (20:10:01)
E		e3roeE1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: V-set	F:	ECOD (20:10:01)
D		e3roeD1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: V-set	F:	ECOD (20:10:01)
B		e3roeB1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: V-set	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	YjeF N-terminal domain	CATH (4.3.0)
C	3.40.50.10260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	YjeF N-terminal domain	CATH (4.3.0)
F	3.40.50.10260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	YjeF N-terminal domain	CATH (4.3.0)
E	3.40.50.10260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	YjeF N-terminal domain	CATH (4.3.0)
D	3.40.50.10260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	YjeF N-terminal domain	CATH (4.3.0)
B	3.40.50.10260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	YjeF N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF03853	YjeF-related protein N-terminus (YjeF_N)	YjeF-related protein N-terminus	YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases [1]. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be ...	YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases [1]. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128) [1], where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Apolipoprotein A-I-binding protein	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding isomerase activity NAD(P)HX epimerase activity racemase and epimerase activity catalytic activity identical protein binding protein binding	nicotinamide nucleotide metabolic process nucleoside phosphate metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process regulation of sterol transport nicotinamide nucleotide metabolic process nucleoside phosphate metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process regulation of sterol transport regulation of localization regulation of biological process transport regulation of transport biological regulation lipid localization lipid transport regulation of lipid transport organic hydroxy compound transport establishment of localization localization regulation of lipid localization macromolecule localization regulation of cholesterol efflux cholesterol transport sterol transport regulation of cholesterol transport cholesterol efflux metabolite repair multicellular organismal process regulation of developmental process negative regulation of biological process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis system development blood vessel development developmental process regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process membrane organization cellular component organization cellular localization membrane raft localization localization within membrane membrane raft organization cellular component organization or biogenesis membrane raft distribution sprouting angiogenesis	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell projection cilium plasma membrane bounded cell projection extracellular region cytosol cell body membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell projection cilium plasma membrane bounded cell projection extracellular region cytosol cell body extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR032976	YjeF N-terminal domain-containing protein NAXE-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR036652	YjeF N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR004443	YjeF N-terminal 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.