Structure of PDB 8dqj Chain D Binding Site BS02

Receptor Information

>8dqj Chain D (length=271) Species: 1291540 (Methanomethylophilus alvi)

GTVKYTDAQIQRLREYGNGTYEQKVFEDLASRDAAFSKEMSVASTDNEKK
IKGMIANPSRHGLTQLMNDIADALVAEGFIEVRTPIFISKDALARMTITE
DKPLFKQVFWIDEKRALRPMLAPNLYSVMRDLRDHTDGPVKIFEMGSCFR
KEMHLEEFTMLSLCDMGPRGDATEVLKNYISVVMKAAGLPDYDLVQEESD
VYKETIDVEINGQEVCSAAVGPHYLDAAHDVHEPTSGAGFGLERLLTIRE
KYSTVKKGGASISYLNGAKIN

Ligand information

• Ligand ID: T7Q
• InChI: InChI=1S/C16H14N2O3/c17-12(16(20)21)8-9-5-6-14-11(7-9)15(19)10-3-1-2-4-13(10)18-14/h1-7,12H,8,17H2,(H,18,19)(H,20,21)/p+1/t12-/m0/s1
• InChIKey: NPALYBYZIAGBTE-LBPRGKRZSA-O
• SMILES:
  CACTVS 3.385: [NH3+][CH](Cc1ccc2Nc3ccccc3C(=O)c2c1)C(O)=O
  OpenEye OEToolkits 2.0.7: c1ccc2c(c1)C(=O)c3cc(ccc3N2)CC(C(=O)O)[NH3+]
  CACTVS 3.385: [NH3+][C@@H](Cc1ccc2Nc3ccccc3C(=O)c2c1)C(O)=O
  ACDLabs 12.01: O=C(O)C([NH3+])Cc1cc2C(=O)c3ccccc3Nc2cc1
  OpenEye OEToolkits 2.0.7: c1ccc2c(c1)C(=O)c3cc(ccc3N2)C[C@@H](C(=O)O)[NH3+]
• Formula: C16 H15 N2 O3
• Name: (2~{S})-2-azanyl-3-(9-oxidanylidene-10~{H}-acridin-2-yl)propanoic acid;
  acridone amino acid (RS1)
• PDB chain: 8dqj Chain D Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dqj Structures of Methanomethylophilus alvus Pyrrolysine tRNA-Synthetases Support the Need for De Novo Selections When Altering the Substrate Specificity.
• Resolution: 1.54 Å
• Binding residue (original residue number in PDB): M120 A122 Y126 C168 Y206 S221 G241 G243
• Binding residue (residue number reindexed from 1): M120 A122 Y126 C164 Y202 S217 G237 G239
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0004812 aminoacyl-tRNA ligase activity
• GO:0005524 ATP binding
• GO:0046872 metal ion binding

External links

• PDB: RCSB:8dqj, PDBe:8dqj, PDBj:8dqj
• PDBsum: 8dqj
• PubMed: 36395426
• UniProt: A0A3G3IHP7