5B6J | pdb_00005b6j

Crystal structure of Peptidyl-tRNA hydrolase mutant -H24N from Vibrio cholerae

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d5b6jb_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Peptidyl-tRNA hydrolase-like	automated matches	automated matches	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
A	d5b6ja_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Peptidyl-tRNA hydrolase-like	automated matches	automated matches	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Peptidyl-tRNA hydrolase-like	8074932	3000647	SCOP2B (2022-06-29)
A	SCOP2 Family	Peptidyl-tRNA hydrolase-like	8074931	4000577	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Peptidyl-tRNA hydrolase-like	8074932	3000647	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	Ank, Ank_2, Ank_4, Ank_5	e5b6jB1	A: alpha bundles	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: Ank, Ank_2, Ank_4, Ank_5	ECOD (develop294)
A	Ank, Ank_2, Ank_4, Ank_5	e5b6jA1	A: alpha bundles	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: Ank, Ank_2, Ank_4, Ank_5	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	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 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 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 cellular 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, B	IPR018171	Peptidyl-tRNA hydrolase, conserved site	Conserved Site
A, B	IPR036416	Peptidyl-tRNA hydrolase superfamily	Homologous Superfamily
A, B	IPR001328	Peptidyl-tRNA hydrolase	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

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.