1GGM | pdb_00001ggm

GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH GLYCYL-ADENYLATE

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)
B	d1ggmb1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	Class II aaRS ABD-related	Anticodon-binding domain of Class II aaRS	Glycyl-tRNA synthetase (GlyRS), C-terminal domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ], (Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d1ggmb2	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	Glycyl-tRNA synthetase (GlyRS)	(Thermus thermophilus HB8 ) [TaxId: 300852 ], (Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d1ggma1	Alpha and beta proteins (a/b)	Anticodon-binding domain-like	Class II aaRS ABD-related	Anticodon-binding domain of Class II aaRS	Glycyl-tRNA synthetase (GlyRS), C-terminal domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ], (Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d1ggma2	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	Glycyl-tRNA synthetase (GlyRS)	(Thermus thermophilus HB8 ) [TaxId: 300852 ], (Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035926	3000058	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS ABD-related	8044417	3000465	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8035926	3000058	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS ABD-related	8044417	3000465	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	tRNA-synt_2b	e1ggmB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: tRNA-synt_2b	ECOD (v294.1)
B	HGTP_anticodon	e1ggmB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (v294.1)
A	tRNA-synt_2b	e1ggmA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: tRNA-synt_2b	ECOD (v294.1)
A	HGTP_anticodon	e1ggmA2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-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)
A	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03129	Anticodon binding domain (HGTP_anticodon)	Anticodon binding domain	This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [1] it is probably the anticodon binding domain [2].	Domain
A, B	PF00587	tRNA synthetase class II core domain (G, H, P, S and T) (tRNA-synt_2b)	tRNA synthetase class II core domain (G, H, P, S and T)	tRNA-synt_2b is a family of largely threonyl-tRNA members.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Glycine--tRNA ligase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding organic acid binding glycine binding amino acid binding carboxylic acid binding ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA glycine-tRNA ligase activity catalytic activity ligase activity protein binding protein dimerization activity identical protein 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 glycyl-tRNA aminoacylation 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 glycyl-tRNA aminoacylation metabolic process cellular process macromolecule metabolic process protein metabolic process	glycine-tRNA ligase complex protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex 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	IPR022961	Glycine-tRNA ligase, bacterial	Family
A, B	IPR002315	Glycyl-tRNA synthetase	Family
A, B	IPR004154	Anticodon-binding	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	IPR036621	Anticodon-binding domain superfamily	Homologous Superfamily
A, B	IPR027031	Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2	Family
A, B	IPR033731	Glycyl-tRNA synthetase-like 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.