Structure of PDB 8joz Chain A Binding Site BS02

Receptor Information
>8joz Chain A (length=257) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AQDRNFDDIAEKFSRNIYGTTKGQLRQAILWQDLDRVLAEMGPQKLRVLD
AGGGEGQTAIKMAERGHQVILCDLSAQMIDRAKQAAEAKGVSDNMQFIHC
AAQDVASHLETPVDLILFHAVLEWVADPRSVLQTLWSVLRPGGVLSLMFY
NAHGLLMHNMVAGNFDYVQAGMPKKKKRTLSPDYPRDPAQVYLWLEEAGW
QIMGKTGVRVFHDYLREKHQQRDCYEALLELETRYCRQEPYITLGRYIHV
TARKPQS
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 chain8joz Chain A Residue 301 [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]
PDB8joz Structural basis for the selective methylation of 5-carboxymethoxyuridine in tRNA modification.
Resolution2.22 Å
Binding residue
(original residue number in PDB)		D3 R4 F6 F13 Y18 R26 G52 G53 D73 L74 M78 A101 A102 Q103 H119 A120
Binding residue
(residue number reindexed from 1)		D3 R4 F6 F13 Y18 R26 G52 G53 D73 L74 M78 A101 A102 Q103 H119 A120
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.1.-
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0097697 tRNA (5-carboxymethoxyuridine(34)-5-O)-methyltransferase activity
Biological Process
GO:0002098 tRNA wobble uridine modification
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8joz, PDBe:8joz, PDBj:8joz
PDBsum8joz
PubMed37587716
UniProtP36566|CMOM_ECOLI tRNA 5-carboxymethoxyuridine methyltransferase (Gene Name=cmoM)

[Back to BioLiP]