2DU7 | pdb_00002du7

Crystal structure of Methanococcus jannacshii O-phosphoseryl-tRNA synthetase

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
D	Flavodoxin_2	e2du7D1	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: Flavodoxin_2	ECOD (v294.1)
C	Flavodoxin_2	e2du7C1	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: Flavodoxin_2	ECOD (v294.1)
B	Flavodoxin_2	e2du7B1	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: Flavodoxin_2	ECOD (v294.1)
A	tRNA-synt_2d	e2du7A1	A: a/b three-layered sandwiches	X: barrel domains in phase 1 flagellin	H: Class II aaRS and biotin synthetases	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2d	ECOD (v294.1)
A		e2du7A2	A: a/b three-layered sandwiches	X: barrel domains in phase 1 flagellin	H: barrel domains in phase 1 flagellin	T: barrel domains in phase 1 flagellin	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
C	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01409	tRNA synthetases class II core domain (F) (tRNA-synt_2d)	tRNA synthetases class II core domain (F)	Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain.	Domain
A, B, C, D	PF18006	O-phosphoseryl-tRNA synthetase C-terminal domain (SepRS_C)	O-phosphoseryl-tRNA synthetase C-terminal domain	The SSHS domain is mainly found in Archaea. The domain makes up part of the anticodon binding domain at the C-terminal of O-phosphoserine--tRNA(Cys) ligase [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	O-phosphoseryl-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 catalytic activity, acting on a nucleic acid phenylalanine-tRNA ligase activity catalytic activity, acting on a tRNA catalytic activity ligase activity phosphoserine-tRNA(Cys) ligase activity RNA binding tRNA binding nucleic acid binding	amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid 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 biosynthetic process amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid 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 biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process phenylalanyl-tRNA aminoacylation	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, B, C, D	IPR005246	O-phosphoseryl-tRNA(Cys) ligase	Family
A, B, C, D	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B, C, D	IPR002319	Phenylalanyl-tRNA synthetase	Domain
A, B, C, D	IPR041590	O-phosphoserine--tRNA(Cys) ligase, C-terminal 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.