2AKW | pdb_00002akw

Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with p-Cl-Phenylalanine

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	d2akwa_	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2akwb1	All alpha proteins	Putative DNA-binding domain	Putative DNA-binding domain	Domains B1 and B5 of PheRS-beta, PheT	Domains B1 and B5 of PheRS-beta, PheT	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2akwb3	All beta proteins	OB-fold	Nucleic acid-binding proteins	Myf domain	Domain B2 of PheRS-beta, PheT	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2akwb4	All beta proteins	PheT/TilS domain	PheT/TilS domain	B3/B4 domain of PheRS, PheT	B3/B4 domain of PheRS, PheT	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2akwb5	Alpha and beta proteins (a+b)	Ferredoxin-like	Anticodon-binding domain of PheRS	Anticodon-binding domain of PheRS	Phenylalanyl-tRNA synthetase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2akwb6	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Phenyl-tRNA synthetase (PheRS) beta subunit, PheT, central domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8101535	3000058	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8037048	3000058	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8037045	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Putative DNA-binding domain	8037042	3000158	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Putative DNA-binding domain	8037043	3000158	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PheT/TilS domain	8037049	3000688	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Putative DNA-binding domain	8037043	3000158	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Anticodon-binding domain of PheRS	8037047	3001309	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	tRNA-synt_2b	e2akwA1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: tRNA-synt_2b	ECOD (develop294)
B	CSD	e2akwB1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CSD	ECOD (develop294)
B	Acyl-CoA_dh_M	e2akwB2	A: alpha bundles	X: EGF-like	H: PABC(PABP) domain	T: PABC(PABP) domain	F: Acyl-CoA_dh_M	ECOD (develop294)
B	MerR-DNA-bind, MerR_1	e2akwB3	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: MerR-DNA-bind, MerR_1	ECOD (develop294)
B	ABM	e2akwB5	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: ABM	ECOD (develop294)
B	tRNA-synt_2b	e2akwB6	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: tRNA-synt_2b	ECOD (develop294)

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 (4.3.0)
B	3.30.56.10	Alpha Beta	2-Layer Sandwich	Phenylalanyl-tRNA Synthetase	Chain B, domain 1	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	3.50.40.10	Alpha Beta	3-Layer(bba) Sandwich	Phenylalanyl-tRNA Synthetase	Chain B, domain 3	CATH (4.3.0)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	3.30.70.380	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Ferrodoxin-fold anticodon-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF03483	B3/4 domain (B3_4)	B3/4 domain	This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins.	Domain
B	PF03484	tRNA synthetase B5 domain (B5)	tRNA synthetase B5 domain	This domain is found in phenylalanine-tRNA synthetase beta subunits.	Domain
B	PF03147	Ferredoxin-fold anticodon binding domain (FDX-ACB)	Ferredoxin-fold anticodon binding domain	This is the anticodon binding domain found in some phenylalanyl tRNA synthetases. The domain has a ferredoxin fold [1,2].	Domain
B	PF17759	Phenylalanyl tRNA synthetase beta chain CLM domain (tRNA_synthFbeta)	Phenylalanyl tRNA synthetase beta chain CLM domain	This domain corresponds to the catalytic like domain (CLM) in the beta chain of phe tRNA synthetase [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Phenylalanyl-tRNA synthetase alpha chain	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid phenylalanine-tRNA ligase activity catalytic activity, acting on a tRNA catalytic activity ligase activity RNA binding tRNA binding nucleic acid binding	amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process 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 phenylalanyl-tRNA aminoacylation	cellular anatomical structure intracellular anatomical structure cytoplasm
B	Phenylalanyl-tRNA synthetase beta chain	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid phenylalanine-tRNA ligase activity catalytic activity, acting on a tRNA catalytic activity ligase activity RNA binding tRNA binding nucleic acid binding	amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process 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 phenylalanyl-tRNA aminoacylation	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex cytoplasm phenylalanine-tRNA ligase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A	IPR002319	Phenylalanyl-tRNA synthetase	Domain
A	IPR004188	Phenylalanine-tRNA ligase, class II, N-terminal	Domain
A	IPR004529	Phenylalanyl-tRNA synthetase, class IIc, alpha subunit	Family
A	IPR022911	Phenylalanine-tRNA ligase alpha chain 1, bacterial	Family
A	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A	IPR010978	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm	Homologous Superfamily
B	IPR009061	Putative DNA-binding domain superfamily	Homologous Superfamily
B	IPR045060	Phenylalanine-tRNA ligase, class IIc, beta subunit	Family
B	IPR020825	Phenylalanyl-tRNA synthetase-like, B3/B4	Homologous Superfamily
B	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
B	IPR002547	tRNA-binding domain	Domain
B	IPR005147	tRNA synthetase, B5-domain	Domain
B	IPR005146	B3/B4 tRNA-binding domain	Domain
B	IPR041616	Phenylalanyl tRNA synthetase beta chain, core domain	Domain
B	IPR033714	Phenylalanly tRNA synthetase, tRNA-binding-domain	Domain
B	IPR005121	Ferrodoxin-fold anticodon-binding domain	Domain
B	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
B	IPR036690	Ferrodoxin-fold anticodon-binding domain superfamily	Homologous Superfamily
B	IPR004532	Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type	Family