1OKJ | pdb_00001okj

crystal structure of the essential E. coli YeaZ protein by MAD method using the gadolinium complex "DOTMA"

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	d1okjd1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	YeaZ-like	Hypothetical protein YeaZ	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d1okjd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d1okjc1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	YeaZ-like	Hypothetical protein YeaZ	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d1okjc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d1okjb1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	YeaZ-like	Hypothetical protein YeaZ	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d1okjb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d1okja1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	YeaZ-like	Hypothetical protein YeaZ	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d1okja3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	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	8038085	3000092	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Actin-like ATPases	8038089	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	8038085	3000092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Actin-like ATPases	8038089	3000092	SCOP2B (2022-06-29)
A	SCOP2 Family	YeaZ-like	8025706	4002236	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Actin-like ATPases	8038089	3000092	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Actin-like ATPases	8038085	3000092	SCOP2 (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	Thioredoxin	e1okjD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Thioredoxin	ECOD (v294.1)
C	Thioredoxin	e1okjC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Thioredoxin	ECOD (v294.1)
B	Thioredoxin	e1okjB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Thioredoxin	ECOD (v294.1)
A	TsaD	e1okjA1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: TsaD	ECOD (v294.1)

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
A, B, C, D	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
A, B, 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR022496	tRNA threonylcarbamoyl adenosine modification protein TsaB	Family
A, B, C, D	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, B, C, D	IPR000905	Gcp-like domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.