3VJR | pdb_00003vjr

Crystal structure of Peptidyl-tRNA hydrolase from Escherichia coli in complex with the CCA-acceptor-T[PSI]C domain of tRNA

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Peptidyl-tRNA hydrolase-like	8044568	3000647	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Peptidyl-tRNA hydrolase-like	8044568	3000647	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	Pept_tRNA_hydro	e3vjrC1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: Pept_tRNA_hydro	ECOD (1.6)
A	Pept_tRNA_hydro	e3vjrA1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: Pept_tRNA_hydro	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.1470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Peptidyl-tRNA hydrolase	CATH (4.3.0)
A	3.40.50.1470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Peptidyl-tRNA hydrolase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF01195	Peptidyl-tRNA hydrolase (Pept_tRNA_hydro)	Peptidyl-tRNA hydrolase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	tRNA CCA-acceptor	-	-	-
A, C	Peptidyl-tRNA hydrolase	hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid carboxylic ester hydrolase activity hydrolase activity catalytic activity, acting on a tRNA peptidyl-tRNA hydrolase activity catalytic activity RNA binding binding tRNA binding nucleic acid binding	cellular component disassembly ribosome disassembly rescue of stalled ribosome primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process cellular component organization organelle organization organelle disassembly biosynthetic process translational elongation cellular process cellular component disassembly ribosome disassembly rescue of stalled ribosome primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process cellular component organization organelle organization organelle disassembly biosynthetic process translational elongation cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process protein metabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process proteolysis protein quality control for misfolded or incompletely synthesized proteins	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR018171	Peptidyl-tRNA hydrolase, conserved site	Conserved Site
A, C	IPR036416	Peptidyl-tRNA hydrolase superfamily	Homologous Superfamily
A, C	IPR001328	Peptidyl-tRNA hydrolase	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.