Structure of PDB 5gm8 Chain A Binding Site BS01

Receptor Information

>5gm8 Chain A (length=170) Species: 287 (Pseudomonas aeruginosa)

QSMMLDRIRVVLVNTSHPGNIGGAARAMKNMGLSQLVLVQPESFPHGDAV
ARASGATDILDAARVVDTLEEALSGCSVVLGTSARDRRIPWPLLDPRECA
TTCLEHLEANGEVALVFGREYAGLTNEELQRCQFHVHIPSDPEFGSLNLA
AAVQVLTYEVRMAWLAAQGK

Ligand information

• Ligand ID: SFG
• InChI: InChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
• InChIKey: LMXOHSDXUQEUSF-YECHIGJVSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
  CACTVS 3.370: N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  CACTVS 3.370: N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  ACDLabs 12.01: O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C15 H23 N7 O5
• Name: SINEFUNGIN;
  ADENOSYL-ORNITHINE
• ChEMBL: CHEMBL1214186
• DrugBank: DB01910
• ZINC: ZINC000004217451
• PDB chain: 5gm8 Chain A Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5gm8 Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): T79 S80 A81 R82 F114 G115 R116 E117 H134 I135 L144 A149
• Binding residue (residue number reindexed from 1): T82 S83 A84 R85 F117 G118 R119 E120 H137 I138 L147 A152
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 2.1.1.200: tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase.

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0008173 RNA methyltransferase activity

Biological Process

• GO:0006396 RNA processing

External links

• PDB: RCSB:5gm8, PDBe:5gm8, PDBj:5gm8
• PDBsum: 5gm8
• PubMed: 27683218
• UniProt: A0A072ZPM2