4YDU | pdb_00004ydu

Crystal structure of E. coli YgjD-YeaZ heterodimer in complex with ADP

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)
D	d4ydud1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d4yduc1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Actin-like ATPases	8038089	3000092	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Actin-like ATPases	8038085	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8038089	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8038085	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8089302	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8092429	3000092	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Actin-like ATPases	8089302	3000092	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Actin-like ATPases	8092429	3000092	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		e4yduD1	A: Anticodon-binding domain of Class II aaRS	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Flavodoxin_2	F:	ECOD (20:10:01)
C		e4yduC1	A: P-loop domains-like	X: P-loop domains-related	H: P-loop containing nucleoside triphosphate hydrolases	T: Nop10p	F:	ECOD (20:10:01)
B		e4yduB1	A: P-loop domains-like	X: P-loop domains-related	H: P-loop containing nucleoside triphosphate hydrolases	T: Nop10p	F:	ECOD (20:10:01)
A		e4yduA1	A: Anticodon-binding domain of Class II aaRS	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Flavodoxin_2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF00814	tRNA N6-adenosine threonylcarbamoyltransferase (TsaD)	tRNA N6-adenosine threonylcarbamoyltransferase	-	Family
A, B	PF00814	tRNA N6-adenosine threonylcarbamoyltransferase (TsaD)	tRNA N6-adenosine threonylcarbamoyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	tRNA threonylcarbamoyladenosine biosynthesis protein TsaB	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity identical protein binding protein binding binding	tRNA threonylcarbamoyladenosine modification tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing tRNA threonylcarbamoyladenosine modification tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification metabolic process cellular process macromolecule metabolic process RNA processing maintenance of translational fidelity translation protein biosynthetic process protein metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex transferase complex EKC/KEOPS complex
A, B	tRNA N6-adenosine threonylcarbamoyltransferase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding tRNA N(6)-L-threonylcarbamoyladenine synthase activity acyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding tRNA N(6)-L-threonylcarbamoyladenine synthase activity acyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity transition metal ion binding iron ion binding protein binding modification-dependent protein binding glycosylation-dependent protein binding identical protein binding	tRNA threonylcarbamoyladenosine modification tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing tRNA threonylcarbamoyladenosine modification tRNA modification RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification metabolic process cellular process macromolecule metabolic process RNA processing maintenance of translational fidelity translation protein biosynthetic process protein metabolic process	protein-containing complex catalytic complex transferase complex EKC/KEOPS complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR022496	tRNA threonylcarbamoyl adenosine modification protein TsaB	Family
C, D	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
C, D	IPR000905	Gcp-like domain	Domain
A, B	IPR022450	tRNA N6-adenosine threonylcarbamoyltransferase, TsaD	Family
A, B	IPR017860	Peptidase M22, conserved site	Conserved Site
A, B	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, B	IPR000905	Gcp-like domain	Domain
A, B	IPR017861	Kae1/TsaD family	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.