5XII

Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with inhibitor 6

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ProRS-C_1	e5xiiA2	A: a+b two layers	X: IF3-like	H: C-terminal domain of ProRS (From Topology)	T: C-terminal domain of ProRS	F: ProRS-C_1	ECOD (1.6)
A	tRNA-synt_2b	e5xiiA1	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2b	ECOD (1.6)
A	HGTP_anticodon	e5xiiA3	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS (From Topology)	H: Anticodon-binding domain of Class II aaRS (From Topology)	T: Anticodon-binding domain of Class II aaRS	F: HGTP_anticodon	ECOD (1.6)
B	ProRS-C_1	e5xiiB1	A: a+b two layers	X: IF3-like	H: C-terminal domain of ProRS (From Topology)	T: C-terminal domain of ProRS	F: ProRS-C_1	ECOD (1.6)
B	tRNA-synt_2b	e5xiiB3	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2b	ECOD (1.6)
B	HGTP_anticodon	e5xiiB2	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS (From Topology)	H: Anticodon-binding domain of Class II aaRS (From Topology)	T: Anticodon-binding domain of Class II aaRS	F: HGTP_anticodon	ECOD (1.6)
D	ProRS-C_1	e5xiiD1	A: a+b two layers	X: IF3-like	H: C-terminal domain of ProRS (From Topology)	T: C-terminal domain of ProRS	F: ProRS-C_1	ECOD (1.6)
D	tRNA-synt_2b	e5xiiD2	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2b	ECOD (1.6)
D	HGTP_anticodon	e5xiiD3	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS (From Topology)	H: Anticodon-binding domain of Class II aaRS (From Topology)	T: Anticodon-binding domain of Class II aaRS	F: HGTP_anticodon	ECOD (1.6)
C	ProRS-C_1	e5xiiC1	A: a+b two layers	X: IF3-like	H: C-terminal domain of ProRS (From Topology)	T: C-terminal domain of ProRS	F: ProRS-C_1	ECOD (1.6)
C	tRNA-synt_2b	e5xiiC2	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2b	ECOD (1.6)
C	HGTP_anticodon	e5xiiC3	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS (From Topology)	H: Anticodon-binding domain of Class II aaRS (From Topology)	T: Anticodon-binding domain of Class II aaRS	F: HGTP_anticodon	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (utative)
A	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (utative)
A	3.30.110.30	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	C-terminal domain of ProRS	CATH (utative)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (utative)
B	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (utative)
B	3.30.110.30	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	C-terminal domain of ProRS	CATH (utative)
D	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (utative)
D	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (utative)
D	3.30.110.30	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	C-terminal domain of ProRS	CATH (utative)
C	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (utative)
C	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (utative)
C	3.30.110.30	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	C-terminal domain of ProRS	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03129	Anticodon binding domain (HGTP_anticodon)	Anticodon binding domain	This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [1] it is probably the anticodon binding domain [2].	Domain
A, B, C, D	PF00587	tRNA synthetase class II core domain (G, H, P, S and T) (tRNA-synt_2b)	tRNA synthetase class II core domain (G, H, P, S and T)	tRNA-synt_2b is a family of largely threonyl-tRNA members.	Domain
A, B, C, D	PF09180	Prolyl-tRNA synthetase, C-terminal (ProRS-C_1)	Prolyl-tRNA synthetase, C-terminal	Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-be ...	Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-beta motif [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Prolyl-tRNA synthetase (ProRS)	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 hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid carboxylic ester hydrolase activity aminoacyl-tRNA editing activity hydrolase activity catalytic activity, acting on a tRNA catalytic activity ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity proline-tRNA ligase activity ligase activity	prolyl-tRNA aminoacylation amino acid activation tRNA aminoacylation cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process prolyl-tRNA aminoacylation amino acid activation tRNA aminoacylation cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR007214	YbaK/aminoacyl-tRNA synthetase-associated domain	Domain
A, B, C, D	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B, C, D	IPR036754	YbaK/aminoacyl-tRNA synthetase-associated domain superfamily	Homologous Superfamily
A, B, C, D	IPR017449	Prolyl-tRNA synthetase, class II	Homologous Superfamily
A, B, C, D	IPR004154	Anticodon-binding	Domain
A, B, C, D	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, B, C, D	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Domain
A, B, C, D	IPR033721	Prolyl-tRNA synthetase, catalytic domain	Domain
A, B, C, D	IPR036621	Anticodon-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR004499	Proline-tRNA ligase, class IIa, archaeal-type	Family
A, B, C, D	IPR002316	Proline-tRNA ligase, class IIa	Family
A, B, C, D	IPR016061	Proline-tRNA ligase, class II, C-terminal	Domain

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.