Structure of PDB 7yse Chain B Binding Site BS03

Receptor Information

>7yse Chain B (length=299) Species: 83333 (Escherichia coli K-12)

QKFDTRTFQGLILTLQDYWARQGCTIVQPLDMEVGAGTSHPMTCLRELGP
EPMAAAYVQPSRRPTDGRYGENPNRLQHYYQFQVVIKPSPDNIQELYLGS
LKELGMDPTIHDIRFVEDNWENPTLGAWGLGWEVWLNGMEVTQFTYFQQV
GGLECKPVTGEITYGLERLAMYIQGVDSVYDLVWSDGPLGKTTYGDVFHQ
NEVEQSTYNFEYADVDFLFTCFEQYEKEAQQLLALENPLPLPAYERILKA
AHSFNLLDARKAISVTERQRYILRIRTLTKAVAEAYYASREALGFPMCN

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 7yse Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7yse The binding mode of orphan glycyl-tRNA synthetase with tRNA supports the synthetase classification and reveals large domain movements.
• Resolution: 2.907 Å
• Binding residue (original residue number in PDB): D119 E134
• Binding residue (residue number reindexed from 1): D118 E133
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 6.1.1.14: glycine--tRNA ligase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004812 aminoacyl-tRNA ligase activity
• GO:0004820 glycine-tRNA ligase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding

Biological Process

• GO:0006412 translation
• GO:0006426 glycyl-tRNA aminoacylation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0009345 glycine-tRNA ligase complex

External links

• PDB: RCSB:7yse, PDBe:7yse, PDBj:7yse
• PDBsum: 7yse
• PubMed: 36753552
• UniProt: P00960|SYGA_ECOLI Glycine--tRNA ligase alpha subunit (Gene Name=glyQ)