2RD2 | pdb_00002rd2

Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE

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 [auth A]	d2rd2a1	All beta proteins	Ribosomal protein L25-like	Ribosomal protein L25-like	Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain	Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B [auth A]	d2rd2a2	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	Glutaminyl-tRNA synthetase (GlnRS)	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2 Family	Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain	8024432	4002383	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Family	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	8024434	4003807	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Ribosomal protein L25-like	8036811	3001161	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Nucleotidylyl transferase	8036813	3001541	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 [auth A]	Transgly	e2rd2A3	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Transgly	ECOD (develop294)
B [auth A]	Tubulin	e2rd2A5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Tubulin	ECOD (develop294)
B [auth A]	HH_signal	e2rd2A4	A: alpha bundles	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: HH_signal	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B [auth A]	3.90.800.10	Alpha Beta	Alpha-Beta Complex	Glutamyl-tRNA Synthetase	domain 3	CATH (4.3.0)
B [auth A]	1.10.1160.10	Mainly Alpha	Orthogonal Bundle	Glutamyl-tRNA Synthetase	domain 2	CATH (4.3.0)
B [auth A]	2.40.240.10	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF00749	tRNA synthetases class I (E and Q), catalytic domain (tRNA-synt_1c)	tRNA synthetases class I (E and Q), catalytic domain	Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).	Domain
B [auth A]	PF03950	tRNA synthetases class I (E and Q), anti-codon binding domain (tRNA-synt_1c_C)	tRNA synthetases class I (E and Q), anti-codon binding domain	This entry represents the first of the two ribosomal L25-like domains of the anticodon binding domain. Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some o ...	This entry represents the first of the two ribosomal L25-like domains of the anticodon binding domain. Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).	Domain
B [auth A]	PF20974	tRNA synthetases class I (E and Q), anti-codon binding domain (tRNA-synt_1c_C2)	tRNA synthetases class I (E and Q), anti-codon binding domain	This entry represents the second ribosomal L25 like domain which is part of the anticodon binding domain. Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In som ...	This entry represents the second ribosomal L25 like domain which is part of the anticodon binding domain. Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A]	Glutaminyl-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 ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid glutamine-tRNA ligase activity catalytic activity, acting on a tRNA catalytic activity ligase activity	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 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 metabolic process cellular process macromolecule metabolic process protein metabolic process glutamyl-tRNA aminoacylation glutaminyl-tRNA aminoacylation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
A [auth B]	Glutamine tRNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR000924	Glutamyl/glutaminyl-tRNA synthetase	Family
B [auth A]	IPR020061	Glutamine-tRNA ligase, alpha-bundle domain superfamily	Homologous Superfamily
B [auth A]	IPR020058	Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain	Domain
B [auth A]	IPR020056	Large ribosomal subunit protein bL25/Gln-tRNA synthetase, N-terminal	Homologous Superfamily
B [auth A]	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
B [auth A]	IPR049437	tRNA synthetases class I (E and Q), anti-codon binding domain	Domain
B [auth A]	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
B [auth A]	IPR020059	Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain	Domain
B [auth A]	IPR011035	Large ribosomal subunit protein bL25/Gln-tRNA synthetase, anti-codon-binding domain superfamily	Homologous Superfamily
B [auth A]	IPR004514	Glutamine-tRNA synthetase	Family
B [auth A]	IPR022861	Glutamine-tRNA ligase, bacterial	Family
B [auth A]	IPR050132	Glutamine/Glutamate--tRNA Ligase	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.