1GAX

CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE

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)
C [auth A]	d1gaxa4	All alpha proteins	Long alpha-hairpin	tRNA-binding arm	Valyl-tRNA synthetase (ValRS) C-terminal domain	Valyl-tRNA synthetase (ValRS) C-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C [auth A]	d1gaxa5	All alpha proteins	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Valyl-tRNA synthetase (ValRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C [auth A]	d1gaxa2	All beta proteins	ValRS/IleRS/LeuRS editing domain	ValRS/IleRS/LeuRS editing domain	ValRS/IleRS/LeuRS editing domain	Valyl-tRNA synthetase (ValRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C [auth A]	d1gaxa3	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	Valyl-tRNA synthetase (ValRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D [auth B]	d1gaxb4	All alpha proteins	Long alpha-hairpin	tRNA-binding arm	Valyl-tRNA synthetase (ValRS) C-terminal domain	Valyl-tRNA synthetase (ValRS) C-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D [auth B]	d1gaxb5	All alpha proteins	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Valyl-tRNA synthetase (ValRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D [auth B]	d1gaxb2	All beta proteins	ValRS/IleRS/LeuRS editing domain	ValRS/IleRS/LeuRS editing domain	ValRS/IleRS/LeuRS editing domain	Valyl-tRNA synthetase (ValRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D [auth B]	d1gaxb3	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	Valyl-tRNA synthetase (ValRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	8042509	3001786	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	ValRS/IleRS/LeuRS editing domain	8033145	3001115	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	tRNA-binding arm	8042508	3000776	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleotidylyl transferase	8042514	3001541	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleotidylyl transferase	8042514	3001541	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	tRNA-binding arm	8042508	3000776	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Nucleotidylyl transferase	8042514	3001541	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	8042509	3001786	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Nucleotidylyl transferase	8042514	3001541	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	ValRS/IleRS/LeuRS editing domain	8033145	3001115	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)
C [auth A]	tRNA-synt_1_2	e1gaxA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (1.6)
C [auth A]	Anticodon_1,tRNA-synt_1_1st	e1gaxA7	A: alpha bundles	X: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Anticodon_1,tRNA-synt_1_1st	ECOD (1.6)
C [auth A]	Val_tRNA-synt_C	e1gaxA3	A: alpha bundles	X: Long alpha-hairpin	H: tRNA-binding arm (From Topology)	T: tRNA-binding arm	F: Val_tRNA-synt_C	ECOD (1.6)
C [auth A]	valS	e1gaxA5	A: a+b three layers	X: A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	H: A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	T: A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: valS	ECOD (1.6)
C [auth A]	tRNA-synt_1_1st	e1gaxA8	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1_1st	ECOD (1.6)
C [auth A]	MCM_OB_3	e1gaxA6	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: MCM_OB_3	ECOD (1.6)
C [auth A]	tRNA-synt_1_3rd	e1gaxA4	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: tRNA-synt_1_3rd	ECOD (1.6)
D [auth B]	tRNA-synt_1_2	e1gaxB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (1.6)
D [auth B]	Anticodon_1,tRNA-synt_1_1st	e1gaxB7	A: alpha bundles	X: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Anticodon_1,tRNA-synt_1_1st	ECOD (1.6)
D [auth B]	Val_tRNA-synt_C	e1gaxB3	A: alpha bundles	X: Long alpha-hairpin	H: tRNA-binding arm (From Topology)	T: tRNA-binding arm	F: Val_tRNA-synt_C	ECOD (1.6)
D [auth B]	valS	e1gaxB5	A: a+b three layers	X: A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	H: A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	T: A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: valS	ECOD (1.6)
D [auth B]	tRNA-synt_1_1st	e1gaxB8	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1_1st	ECOD (1.6)
D [auth B]	MCM_OB_3	e1gaxB6	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: MCM_OB_3	ECOD (1.6)
D [auth B]	tRNA-synt_1_3rd	e1gaxB4	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: tRNA-synt_1_3rd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
C [auth A]	1.10.730.10	Mainly Alpha	Orthogonal Bundle	Isoleucyl-tRNA Synthetase	Domain 1	CATH (4.3.0)
C [auth A]	3.90.740.10	Alpha Beta	Alpha-Beta Complex	Isoleucyl-tRNA Synthetase	domain 2	CATH (4.3.0)
C [auth A]	3.30.1170.10	Alpha Beta	2-Layer Sandwich	Valyl-trna Synthetase	Chain: A, domain 4	CATH (4.3.0)
C [auth A]	1.10.287.380	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Valyl-tRNA synthetase, C-terminal domain	CATH (4.3.0)
D [auth B]	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
D [auth B]	1.10.730.10	Mainly Alpha	Orthogonal Bundle	Isoleucyl-tRNA Synthetase	Domain 1	CATH (4.3.0)
D [auth B]	3.90.740.10	Alpha Beta	Alpha-Beta Complex	Isoleucyl-tRNA Synthetase	domain 2	CATH (4.3.0)
D [auth B]	3.30.1170.10	Alpha Beta	2-Layer Sandwich	Valyl-trna Synthetase	Chain: A, domain 4	CATH (4.3.0)
D [auth B]	1.10.287.380	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Valyl-tRNA synthetase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF08264	Anticodon-binding domain of tRNA ligase (Anticodon_1)	Anticodon-binding domain of tRNA ligase	This domain is found mainly hydrophobic tRNA synthetases. The domain binds to the anticodon of the tRNA ligase.	Domain
C [auth A], D [auth B]	PF00133	tRNA synthetases class I (I, L, M and V) (tRNA-synt_1)	tRNA synthetases class I (I, L, M and V)	Other tRNA synthetase sub-families are too dissimilar to be included.	Domain
C [auth A], D [auth B]	PF10458	Valyl tRNA synthetase tRNA binding arm (Val_tRNA-synt_C)	Valyl tRNA synthetase tRNA binding arm	This domain is found at the C-terminus of Valyl tRNA synthetases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth D]	TRNA(VAL)	-	-	-
C [auth A], D [auth B]	VALYL-TRNA SYNTHETASE	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 catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA valine-tRNA ligase activity catalytic activity ligase activity hydrolase activity, acting on ester bonds carboxylic ester hydrolase activity aminoacyl-tRNA editing activity hydrolase activity cation binding metal ion binding	amino acid activation tRNA aminoacylation cellular biosynthetic process organonitrogen compound biosynthetic process RNA metabolic process amino acid metabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process protein metabolic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process translation amino acid activation tRNA aminoacylation cellular biosynthetic process organonitrogen compound biosynthetic process RNA metabolic process amino acid metabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process protein metabolic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process biosynthetic process ncRNA metabolic process valyl-tRNA aminoacylation 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
C [auth A], D [auth B]	IPR033705	Valyl tRNA synthetase, anticodon-binding domain	Domain
C [auth A], D [auth B]	IPR037118	Valyl-tRNA synthetase, tRNA-binding arm superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR002303	Valine-tRNA ligase	Family
C [auth A], D [auth B]	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
C [auth A], D [auth B]	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
C [auth A], D [auth B]	IPR002300	Aminoacyl-tRNA synthetase, class Ia	Domain
C [auth A], D [auth B]	IPR019499	Valyl-tRNA synthetase, tRNA-binding arm	Domain
C [auth A], D [auth B]	IPR009008	Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain	Homologous Superfamily
C [auth A], D [auth B]	IPR010978	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm	Homologous Superfamily
C [auth A], D [auth B]	IPR009080	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Homologous Superfamily
C [auth A], D [auth B]	IPR013155	Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.