2DQ0 | pdb_00002dq0

Crystal structure of seryl-tRNA synthetase from Pyrococcus horikoshii complexed with a seryl-adenylate analog

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Seryl_tRNA_N	e2dq0B3	A: alpha bundles	X: Long alpha-hairpin	H: tRNA-binding arm (From Topology)	T: tRNA-binding arm	F: Seryl_tRNA_N	ECOD (1.6)
B	tRNA-synt_2b	e2dq0B2	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2b	ECOD (1.6)
A	Seryl_tRNA_N	e2dq0A2	A: alpha bundles	X: Long alpha-hairpin	H: tRNA-binding arm (From Topology)	T: tRNA-binding arm	F: Seryl_tRNA_N	ECOD (1.6)
A	tRNA-synt_2b	e2dq0A3	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2b	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.287.40	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Serine-tRNA synthetase, tRNA binding domain	CATH (4.2.0)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.2.0)
A	1.10.287.40	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Serine-tRNA synthetase, tRNA binding domain	CATH (4.2.0)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Seryl-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 ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA serine-tRNA ligase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity	small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process selenocysteine biosynthetic process amino acid metabolic process primary metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process selenocysteine metabolic process amino acid biosynthetic process biosynthetic process small molecule metabolic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process selenocysteine biosynthetic process amino acid metabolic process primary metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process selenocysteine metabolic process amino acid biosynthetic process biosynthetic process small molecule metabolic process metabolic process cellular process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process amino acid activation tRNA aminoacylation RNA 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 seryl-tRNA aminoacylation macromolecule metabolic process protein metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B	IPR042103	Serine-tRNA synthetase, type1, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR002317	Serine-tRNA ligase, type1	Family
A, B	IPR015866	Serine-tRNA synthetase, type1, N-terminal	Domain
A, B	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, B	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Domain
A, B	IPR010978	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm	Homologous Superfamily
A, B	IPR033729	Serine-tRNA ligase catalytic core 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.