2PID | pdb_00002pid

Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog

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)
B	d2pidb_	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)
A	d2pida_	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)
B	SCOP2B Superfamily	Nucleotidylyl transferase	8060034	3001541	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotidylyl transferase	8060034	3001541	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)
B		e2pidB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Rpf1_C	F:	ECOD (20:10:01)
A		e2pidA1	A: Profilin-like	X: sensor domains	H: sensor domains	T: NT5C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

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

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	Tyrosyl-tRNA synthetase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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 tyrosine-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity cation binding organic acid binding L-tyrosine binding amino acid binding carboxylic acid binding RNA binding nucleic acid binding tRNA binding	amino acid activation tyrosyl-tRNA aminoacylation tRNA aminoacylation mitochondrial translation RNA metabolic process amino acid metabolic process mitochondrial gene expression protein biosynthetic process nucleobase-containing compound metabolic process protein metabolic process mitochondrial tyrosyl-tRNA aminoacylation primary metabolic process translation gene expression amino acid activation tyrosyl-tRNA aminoacylation tRNA aminoacylation mitochondrial translation RNA metabolic process amino acid metabolic process mitochondrial gene expression protein biosynthetic process nucleobase-containing compound metabolic process protein metabolic process mitochondrial tyrosyl-tRNA aminoacylation primary metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process tRNA aminoacylation for mitochondrial protein translation biosynthetic process metabolic process cellular process macromolecule metabolic process mitochondrial RNA metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear body membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear body nucleoplasm organelle lumen membraneless organelle 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	IPR002307	Tyrosine-tRNA ligase	Family
A, B	IPR002305	Aminoacyl-tRNA synthetase, class Ic	Family
A, B	IPR024088	Tyrosine-tRNA ligase, bacterial-type	Family
A, B	IPR036986	RNA-binding S4 domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9Y2Z4	myopathy, lactic acidosis, and sideroblastic anemia 2 myopathy, lactic acidosis, and sideroblastic anemia arthrogryposis congenital anemia lung cancer myopathy, lactic acidosis, and sideroblastic anemia 1 atrial fibrillation Congenital myopathy (disorder) breast cancer ovarian cancer

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.