3ADB | pdb_00003adb

Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 1)

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)
B	SCOP2B Superfamily	PstK C-terminal domain-like	8056737	3002358	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8019170	3002021	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PstK C-terminal domain-like	8056737	3002358	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8019170	3002021	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)
B	KTI12	e3adbB1	A: alpha bundles	X: alpha-helical domain in AF1104-like proteins (From Topology)	H: alpha-helical domain in AF1104-like proteins (From Topology)	T: alpha-helical domain in AF1104-like proteins	F: KTI12	ECOD (1.6)
B	AAA_33	e3adbB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_33	ECOD (1.6)
A	KTI12	e3adbA1	A: alpha bundles	X: alpha-helical domain in AF1104-like proteins (From Topology)	H: alpha-helical domain in AF1104-like proteins (From Topology)	T: alpha-helical domain in AF1104-like proteins	F: KTI12	ECOD (1.6)
A	AAA_33	e3adbA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_33	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.12.40	Mainly Alpha	Orthogonal Bundle	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.12.40	Mainly Alpha	Orthogonal Bundle	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08433	Chromatin associated protein KTI12 (KTI12)	Chromatin associated protein KTI12	This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II [1]. The Elongator complex has histone acetyltransferase activity.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	selenocysteine tRNA	-	-	-
A, B	L-seryl-tRNA(Sec) kinase	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 L-seryl-tRNA(Sec) kinase activity kinase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	conversion of seryl-tRNAsec to selenocys-tRNAsec 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 conversion of seryl-tRNAsec to selenocys-tRNAsec 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 charged-tRNA amino acid modification macromolecule metabolic process RNA processing tRNA wobble uridine modification tRNA wobble base modification	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR013641	Protein KTI12/L-seryl-tRNA(Sec) kinase	Family
A, B	IPR052648	L-seryl-tRNA(Sec) kinase	Family
A, B	IPR020024	L-seryl-tRNA(Sec) kinase, archaea	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.