Structure of PDB 5gm8 Chain C Binding Site BS01

Receptor Information
>5gm8 Chain C (length=170) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QSMMLDRIRVVLVNTSHPGNIGGAARAMKNMGLSQLVLVQPESFPHGDAV
ARASGATDILDAARVVDTLEEALSGCSVVLGTSARDRRIPWPLLDPRECA
TTCLEHLEANGEVALVFGREYAGLTNEELQRCQFHVHIPSDPEFGSLNLA
AAVQVLTYEVRMAWLAAQGK
Ligand information
Ligand IDSFG
InChIInChI=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
InChIKeyLMXOHSDXUQEUSF-YECHIGJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(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 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
CACTVS 3.370N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370N[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 12.01O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N7 O5
NameSINEFUNGIN;
ADENOSYL-ORNITHINE
ChEMBLCHEMBL1214186
DrugBankDB01910
ZINCZINC000004217451
PDB chain5gm8 Chain C Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5gm8 Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		T79 S80 A81 R82 F114 G115 R116 E117 Y118 G120 H134 I135 S143 L144 A149
Binding residue
(residue number reindexed from 1)		T82 S83 A84 R85 F117 G118 R119 E120 Y121 G123 H137 I138 S146 L147 A152
Annotation score3
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5gm8, PDBe:5gm8, PDBj:5gm8
PDBsum5gm8
PubMed27683218
UniProtA0A072ZPM2

[Back to BioLiP]