2CX5 | pdb_00002cx5

Crystal structure of a putative trans-editing enzyme for prolyl tRNA synthetase

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)
D	d2cx5d_	Alpha and beta proteins (a+b)	YbaK/ProRS associated domain	YbaK/ProRS associated domain	automated matches	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C	d2cx5c_	Alpha and beta proteins (a+b)	YbaK/ProRS associated domain	YbaK/ProRS associated domain	automated matches	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d2cx5b_	Alpha and beta proteins (a+b)	YbaK/ProRS associated domain	YbaK/ProRS associated domain	automated matches	automated matches	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d2cx5a_	Alpha and beta proteins (a+b)	YbaK/ProRS associated domain	YbaK/ProRS associated domain	automated matches	automated matches	(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)
D	SCOP2B Superfamily	ProX-like	8081270	3000535	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ProX-like	8081270	3000535	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ProX-like	8081270	3000535	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ProX-like	8081270	3000535	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)
D	MATH_2	e2cx5D1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
C	MATH_2	e2cx5C1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
B	MATH_2	e2cx5B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
A	EF-hand_6	e2cx5A1	A: a/b three-layered sandwiches	X: Globin-like	H: Globin-like	T: Globin-like	F: EF-hand_6	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.960.10	Alpha Beta	Alpha-Beta Complex	YbaK protein	YbaK/aminoacyl-tRNA synthetase-associated domain	CATH (4.3.0)
C	3.90.960.10	Alpha Beta	Alpha-Beta Complex	YbaK protein	YbaK/aminoacyl-tRNA synthetase-associated domain	CATH (4.3.0)
B	3.90.960.10	Alpha Beta	Alpha-Beta Complex	YbaK protein	YbaK/aminoacyl-tRNA synthetase-associated domain	CATH (4.3.0)
A	3.90.960.10	Alpha Beta	Alpha-Beta Complex	YbaK protein	YbaK/aminoacyl-tRNA synthetase-associated domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF04073	Aminoacyl-tRNA editing domain (tRNA_edit)	Aminoacyl-tRNA editing domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	A PUTATIVE TRANS-EDITING ENZYME	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	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR007214	YbaK/aminoacyl-tRNA synthetase-associated domain	Domain
A, B, C, D	IPR036754	YbaK/aminoacyl-tRNA synthetase-associated domain superfamily	Homologous Superfamily

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.