1IL2 | pdb_00001il2

Crystal Structure of the E. coli Aspartyl-tRNA Synthetase:Yeast tRNAasp:aspartyl-Adenylate Complex

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)
C [auth A]	d1il2a1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Anticodon-binding domain	Aspartyl-tRNA synthetase (AspRS)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C [auth A]	d1il2a2	Alpha and beta proteins (a+b)	DCoH-like	GAD domain-like	GAD domain	Prokaryotic AspRS, insert domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C [auth A]	d1il2a3	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)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth B]	d1il2b1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Anticodon-binding domain	Aspartyl-tRNA synthetase (AspRS)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth B]	d1il2b2	Alpha and beta proteins (a+b)	DCoH-like	GAD domain-like	GAD domain	Prokaryotic AspRS, insert domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth B]	d1il2b3	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)	(Escherichia coli ) [TaxId: 562 ],	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	8041912	3000135	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	GAD domain-like	8035912	3000108	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035966	3000058	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035966	3000058	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	GAD domain-like	8035912	3000108	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035966	3000058	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035966	3000058	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Nucleic acid-binding proteins	8041912	3000135	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]		e1il2A1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: CSD	F:	ECOD (20:10:01)
C [auth A]		e1il2A2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
C [auth A]		e1il2A3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Pkinase	F:	ECOD (20:10:01)
D [auth B]		e1il2B1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: CSD	F:	ECOD (20:10:01)
D [auth B]		e1il2B2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
D [auth B]		e1il2B3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Pkinase	F:	ECOD (20:10:01)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF02938	GAD domain (GAD)	GAD domain	This domain is found in some members of the GatB and aspartyl tRNA synthetases.	Domain
C [auth A], D [auth B]	PF00152	tRNA synthetases class II (D, K and N) (tRNA-synt_2)	tRNA synthetases class II (D, K and N)		Domain
C [auth A], D [auth B]	PF01336	OB-fold nucleic acid binding domain (tRNA_anti-codon)	OB-fold nucleic acid binding domain	This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an am ...	This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family [2,3]. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth D]	ASPARTYL TRANSFER RNA	-	-	-
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 cytosol

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.