1EFW | pdb_00001efw

Crystal structure of aspartyl-tRNA synthetase from Thermus thermophilus complexed to tRNAasp from Escherichia coli

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 [auth A]	d1efwa1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Anticodon-binding domain	Aspartyl-tRNA synthetase (AspRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C [auth A]	d1efwa2	Alpha and beta proteins (a+b)	DCoH-like	GAD domain-like	GAD domain	Prokaryotic AspRS, insert domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C [auth A]	d1efwa3	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	Aspartyl-tRNA synthetase (AspRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D [auth B]	d1efwb1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Anticodon-binding domain	Aspartyl-tRNA synthetase (AspRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D [auth B]	d1efwb2	Alpha and beta proteins (a+b)	DCoH-like	GAD domain-like	GAD domain	Prokaryotic AspRS, insert domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D [auth B]	d1efwb3	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	Aspartyl-tRNA synthetase (AspRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	Nucleic acid-binding proteins	8040930	3000135	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8040932	3000058	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	GAD domain-like	8040931	3000108	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8040932	3000058	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	GAD domain-like	8040931	3000108	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8040932	3000058	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Nucleic acid-binding proteins	8040930	3000135	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8040932	3000058	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 [auth A]	CSD	e1efwA1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: CSD	ECOD (v294.1)
C [auth A]	tRNA_int_endo_N	e1efwA2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: tRNA_int_endo_N	ECOD (v294.1)
C [auth A]	tRNA-synt_2b	e1efwA3	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: tRNA-synt_2b	ECOD (v294.1)
D [auth B]	CSD	e1efwB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: CSD	ECOD (v294.1)
D [auth B]	tRNA_int_endo_N	e1efwB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: tRNA_int_endo_N	ECOD (v294.1)
D [auth B]	tRNA-synt_2b	e1efwB3	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)
C [auth A]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C [auth A]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
C [auth A]	3.30.1360.30	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
D [auth B]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
D [auth B]	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
D [auth B]	3.30.1360.30	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A], D [auth B]	ASPARTYL-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 nucleic acid binding ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA aspartate-tRNA ligase activity catalytic activity ligase activity	amino acid activation aspartyl-tRNA aminoacylation 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 amino acid activation aspartyl-tRNA aminoacylation 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 metabolic process cellular process macromolecule metabolic process protein metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
A [auth C], B [auth D]	ASPARTYL-TRNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
C [auth A], D [auth B]	IPR002312	Aspartyl/Asparaginyl-tRNA synthetase, class IIb	Family
C [auth A], D [auth B]	IPR047089	Aspartate-tRNA ligase, type 1, anticodon recognition domain	Domain
C [auth A], D [auth B]	IPR047090	Aspartate-tRNA ligase, type 1, core domain	Domain
C [auth A], D [auth B]	IPR004365	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type	Domain
C [auth A], D [auth B]	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
C [auth A], D [auth B]	IPR029351	GAD domain	Domain
C [auth A], D [auth B]	IPR004115	GAD-like domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
C [auth A], D [auth B]	IPR004364	Aminoacyl-tRNA synthetase, class II (D/K/N)	Domain
C [auth A], D [auth B]	IPR004524	Aspartate-tRNA ligase, type 1	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.