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	Rrf2	e3vjrC1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: Rrf2	ECOD (develop294)
A	Cytochrom_C	e3vjrA1	A: alpha bundles	X: Flavodoxin-like	H: Precorrin-8X methylmutase CbiC/CobH	T: Precorrin-8X methylmutase CbiC/CobH	F: Cytochrom_C	ECOD (develop294)

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 response to stimulus cellular response to antibiotic cellular response to chemical stimulus response to stimulus response to chemical cellular process response to antibiotic cellular component disassembly ribosome disassembly primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process cellular response to stimulus cellular response to antibiotic cellular response to chemical stimulus response to stimulus response to chemical cellular process response to antibiotic cellular component disassembly ribosome disassembly primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process cellular component organization organelle organization biosynthetic process organelle disassembly translational elongation cytoplasmic translation metabolic process cytoplasmic translational elongation protein metabolic process macromolecule metabolic process cellular component organization or biogenesis rescue of stalled cytosolic ribosome catabolic process protein catabolic process protein quality control for misfolded or incompletely synthesized proteins macromolecule catabolic process	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.