1SES | pdb_00001ses

CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1sesa1	All alpha proteins	Long alpha-hairpin	tRNA-binding arm	Seryl-tRNA synthetase (SerRS)	Seryl-tRNA synthetase (SerRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d1sesa2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Seryl-tRNA synthetase (SerRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1sesb1	All alpha proteins	Long alpha-hairpin	tRNA-binding arm	Seryl-tRNA synthetase (SerRS)	Seryl-tRNA synthetase (SerRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1sesb2	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	Seryl-tRNA synthetase (SerRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	tRNA-binding arm	8036318	3000776	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035887	3000058	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035887	3000058	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	tRNA-binding arm	8036318	3000776	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)
A	Seryl_tRNA_N	e1sesA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: tRNA-binding arm	T: tRNA-binding arm	F: Seryl_tRNA_N	ECOD (v294.1)
A	tRNA-synt_2	e1sesA2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: tRNA-synt_2	ECOD (v294.1)
B	Val_tRNA-synt_C	e1sesB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: tRNA-binding arm	T: tRNA-binding arm	F: Val_tRNA-synt_C	ECOD (v294.1)
B	tRNA-synt_2	e1sesB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: tRNA-synt_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.287.40	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Serine-tRNA synthetase, tRNA binding domain	CATH (4.3.0)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	1.10.287.40	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Serine-tRNA synthetase, tRNA binding domain	CATH (4.3.0)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)

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 identical protein binding protein binding protein homodimerization activity protein dimerization activity cation binding organic acid binding serine binding amino acid binding carboxylic acid binding RNA binding tRNA binding nucleic acid binding	oxoacid metabolic process small molecule biosynthetic process modified amino acid biosynthetic process carboxylic acid metabolic process modified amino acid metabolic process L-amino acid biosynthetic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process oxoacid metabolic process small molecule biosynthetic process modified amino acid biosynthetic process carboxylic acid metabolic process modified amino acid metabolic process L-amino acid biosynthetic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process small molecule metabolic process L-selenocysteine 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

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	serine---tRNA ligase M-CSA #884	Serine-tRNA ligase (EC:6.1.1.11) exists as monomer and belongs to the aminoacyl-tRNA synthetase class IIa. It catalyses the attachment of serine to tRNA (Ser). It is also able to aminoacylate tRNA (Sec) with serine, to form the misacylated tRNA L-seryl-tRNA (Sec), which will be further converted into selenocysteinyl-tRNA (Sec).	Defined by 5 residues: ARG:A-256ARG:A-271GLU:A-345SER:A-348ARG:A-386 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 6.1.1.11 (PDB Primary Data) Search M-CSA Motif + EC 6.1.1.11

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.

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