1YFR | pdb_00001yfr

crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium

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)
B	d1yfrb1	All alpha proteins	Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d1yfrb2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Alanyl-tRNA synthetase (AlaRS)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d1yfrb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1yfra1	All alpha proteins	Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1yfra2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Alanyl-tRNA synthetase (AlaRS)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1yfra3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8034396	3000058	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	8034395	3001120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8034396	3000058	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	8034395	3001120	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_2	e1yfrB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (v294.1)
B	tRNA-synt_2b	e1yfrB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: tRNA-synt_2b	ECOD (v294.1)
A	Ion_trans_2	e1yfrA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (v294.1)
A	tRNA-synt_2b	e1yfrA2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: tRNA-synt_2b	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01411	tRNA synthetases class II (A) (tRNA-synt_2c)	tRNA synthetases class II (A)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Alanyl-tRNA synthetase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding aminoacyl-tRNA deacylase activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid deacylase activity carboxylic ester hydrolase activity hydrolase activity catalytic activity, acting on a tRNA catalytic activity ligase activity, forming carbon-oxygen bonds alanine-tRNA ligase activity aminoacyl-tRNA ligase activity ligase activity cation binding transition metal ion binding zinc ion binding metal ion binding RNA binding tRNA binding nucleic acid binding	amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process alanyl-tRNA aminoacylation amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process alanyl-tRNA aminoacylation metabolic process cellular process macromolecule metabolic process protein metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B	IPR018164	Alanyl-tRNA synthetase, class IIc, N-terminal	Domain
A, B	IPR018162	Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily	Homologous Superfamily
A, B	IPR003156	DHHA1 domain	Domain
A, B	IPR012947	Threonyl/alanyl tRNA synthetase, SAD	Domain
A, B	IPR002318	Alanine-tRNA ligase, class IIc	Family
A, B	IPR050058	Alanine--tRNA ligase	Family
A, B	IPR018163	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily	Homologous Superfamily
A, B	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, B	IPR018165	Alanyl-tRNA synthetase, class IIc, core domain	Domain
A, B	IPR023033	Alanine-tRNA ligase, eukaryota/bacteria	Family

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.