3A5Y | pdb_00003a5y

Crystal structure of GenX from Escherichia coli in complex with lysyladenylate analog

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8098374	3000058	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8098374	3000058	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8098374	3000058	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8098374	3000058	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)
D	Sdh_cyt	e3a5yD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Sdh_cyt	ECOD (v294.1)
C	Sdh_cyt	e3a5yC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Sdh_cyt	ECOD (v294.1)
B	Sdh_cyt	e3a5yB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Sdh_cyt	ECOD (v294.1)
A	V-set	e3a5yA1	A: a/b three-layered sandwiches	X: Retrovirus capsid protein	H: Ubiquitin-related	T: Ubiquitin-like	F: V-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
C	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00152	tRNA synthetases class II (D, K and N) (tRNA-synt_2)	tRNA synthetases class II (D, K and N)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Putative lysyl-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 identical protein binding protein binding protein homodimerization activity protein dimerization activity 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 lysine-tRNA ligase activity catalytic activity ligase activity acid-ammonia (or amide) ligase activity ligase activity, forming carbon-nitrogen bonds aminoacyltransferase activity protein-lysine lysyltransferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity RNA binding tRNA binding nucleic acid binding	cellular response to stimulus response to stimulus response to pH cellular response to pH response to abiotic stimulus cellular process cellular response to acidic pH response to acidic pH cellular response to abiotic stimulus cellular response to environmental stimulus lysyl-tRNA aminoacylation amino acid activation tRNA aminoacylation RNA metabolic process cellular response to stimulus response to stimulus response to pH cellular response to pH response to abiotic stimulus cellular process cellular response to acidic pH response to acidic pH cellular response to abiotic stimulus cellular response to environmental stimulus lysyl-tRNA aminoacylation 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 macromolecule metabolic process protein metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, B, C, D	IPR018149	Lysyl-tRNA synthetase, class II, C-terminal	Domain
A, B, C, D	IPR004364	Aminoacyl-tRNA synthetase, class II (D/K/N)	Domain
A, B, C, D	IPR004525	Elongation factor P--(R)-beta-lysine ligase	Family

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.