5EKD

Human mitochondrial tryptophanyl-tRNA synthetase bound by indolmycin and Mn*ATP.

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5ekda_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5ekdb_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotidylyl transferase	8070087	3001541	SCOP2B (2022-06-29)
B	SCOP2 Family	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	8070086	4003807	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Nucleotidylyl transferase	8070087	3001541	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)
A	tRNA-synt_1b	e5ekdA1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1b	ECOD (1.6)
B	tRNA-synt_1b	e5ekdB1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1b	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	1.10.240.10	Mainly Alpha	Orthogonal Bundle	Tyrosyl-Transfer RNA Synthetase	Tyrosyl-Transfer RNA Synthetase	CATH (4.3.0)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	1.10.240.10	Mainly Alpha	Orthogonal Bundle	Tyrosyl-Transfer RNA Synthetase	Tyrosyl-Transfer RNA Synthetase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00579	tRNA synthetases class I (W and Y) (tRNA-synt_1b)	tRNA synthetases class I (W and Y)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Tryptophan--tRNA ligase, mitochondrial	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 ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA tryptophan-tRNA ligase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity	developmental process multicellular organismal process cellular developmental process blood vessel morphogenesis tube development vasculogenesis vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis cell differentiation anatomical structure development cellular process developmental process multicellular organismal process cellular developmental process blood vessel morphogenesis tube development vasculogenesis vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis cell differentiation anatomical structure development cellular process blood vessel development system development regulation of developmental process positive regulation of biological process angiogenesis regulation of vasculature development positive regulation of developmental process regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of multicellular organismal development regulation of biological process biological regulation positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis positive regulation of multicellular organismal process amino acid activation tRNA aminoacylation mitochondrial translation cellular biosynthetic process RNA metabolic process amino acid metabolic process mitochondrial gene expression nucleobase-containing compound metabolic process tryptophanyl-tRNA aminoacylation protein metabolic process cellular metabolic process primary metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA aminoacylation for mitochondrial protein translation tRNA metabolic process biosynthetic process metabolic process mitochondrial tryptophanyl-tRNA aminoacylation macromolecule metabolic process mitochondrial RNA metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
A, B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, B	IPR002306	Tryptophan-tRNA ligase	Family
A, B	IPR050203	Tryptophan--tRNA ligase	Family
A, B	IPR002305	Aminoacyl-tRNA synthetase, class Ic	Family
A, B	IPR024109	Tryptophan-tRNA ligase, bacterial-type	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9UGM6	neurodevelopmental disorder, mitochondrial, with abnormal movements and lactic acidosis, with or without seizures invasive ductal breast carcinoma Mitochondrial Diseases ovarian cancer large cell medulloblastoma psoriasis malignant ependymoma osteosarcoma tuberculosis

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.