1WY5

Crystal structure of isoluecyl-tRNA lysidine 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)
A	d1wy5a1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	PP-loop ATPase	TilS-like protein Aq_1887	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1wy5a2	Alpha and beta proteins (a+b)	MesJ substrate recognition domain-like	MesJ substrate recognition domain-like	MesJ substrate recognition domain-like	TilS-like protein Aq_1887	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d1wy5b1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	PP-loop ATPase	TilS-like protein Aq_1887	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d1wy5b2	Alpha and beta proteins (a+b)	MesJ substrate recognition domain-like	MesJ substrate recognition domain-like	MesJ substrate recognition domain-like	TilS-like protein Aq_1887	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PP-loop ATPase	8021009	4002958	SCOP2 (2022-06-29)
A	SCOP2 Family	MesJ substrate recognition domain-like	8021011	4003359	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Adenine nucleotide alpha hydrolases-like	8033389	3001593	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MesJ substrate recognition domain-like	8033391	3000685	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	MesJ substrate recognition domain-like	8033391	3000685	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8033389	3001593	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)
A	PF22132	e1wy5A2	A: a+b two layers	X: MesJ substrate recognition domain-like (From Topology)	H: MesJ substrate recognition domain-like (From Topology)	T: MesJ substrate recognition domain-like	F: PF22132	ECOD (1.6)
A	PF01171	e1wy5A1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: PF01171	ECOD (1.6)
B	PF22132	e1wy5B1	A: a+b two layers	X: MesJ substrate recognition domain-like (From Topology)	H: MesJ substrate recognition domain-like (From Topology)	T: MesJ substrate recognition domain-like	F: PF22132	ECOD (1.6)
B	PF01171	e1wy5B2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: PF01171	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	1.20.59.20	Mainly Alpha	Up-down Bundle	Chorismate Mutase Domain, subunit A		CATH (4.3.0)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	1.20.59.20	Mainly Alpha	Up-down Bundle	Chorismate Mutase Domain, subunit A		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01171	PP-loop family (ATP_bind_3)	PP-loop family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Hypothetical UPF0072 protein AQ_1887	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process RNA modification biosynthetic process ncRNA metabolic process macromolecule modification nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011063	tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal	Domain
A, B	IPR012795	tRNA(Ile)-lysidine synthase, N-terminal	Domain
A, B	IPR012094	tRNA(Ile)-lysidine synthase	Family
A, B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	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 R01GM133198.