Structure of PDB 3v8v Chain A Binding Site BS03

Receptor Information
>3v8v Chain A (length=664) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNSLFASTARGLEELLKTELENLGAVECQVVQGGVHFKGDTRLVYQSLMW
SRLASRIMLPLGECKVYSDLDLYLGVQAINWTEMFNPGATFAVHFSGLND
TIRNSQYGAMKVKDAIVDAFTRKNLPRPNVDRDAPDIRVNVWLHKETASI
ALDLSGDGLHLRGYRDRAGIAPIKETLAAAIVMRSGWQPGTPLLDPMCGS
GTLLIEAAMLATDRAPGLHRGRWGFSGWAQHDEAIWQEVKAEAQTRARKG
LAEYSSHFYGSDSDARVIQRARTNARLAGIGELITFEVKDVAQLTNPLPK
GPYGTVLSNPPYGDSEPALIALHSLLGRIMKNQFGGWNLSLFSASPDLLS
CLQLRADKQYKAKNGPLDCVQKNYHVAEMVAEDYTNRLRKNLKKFEKWAR
QEGIECYRLYDADLPEYNVAVDRYADWVVVQEYAPHKARQRLFDIIAATI
SVLGIAPNKLVLKTREKGEFLEVTEYNAHLWVNLTDYLDTGLFLDHRIAR
RMLGQMSKGKDFLNLFSYTGSATVHAGLGGARSTTTVDMSRTYLEWAERN
LRLNGLTGRAHRLIQADCLAWLREANEQFDLIFIDPPTFAFDVQRDHLAL
MKDLKRLLRAGGTIMFSNNKRGFRMDLDGLAKLGLKAQEITQKTLSQDFA
RNRQIHNCWLITAA
Ligand information
Ligand IDTRV
InChIInChI=1S/C14H26O7/c1-2-3-4-5-6-7-11(16)20-8-10-12(17)13(18)14(19,9-15)21-10/h10,12-13,15,17-19H,2-9H2,1H3/t10-,12-,13+,14-/m1/s1
InChIKeyUJGLCJCSHGMKFA-RUZUBIRVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCCCCCCC(=O)OCC1C(C(C(O1)(CO)O)O)O
CACTVS 3.385CCCCCCCC(=O)OC[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 2.0.7CCCCCCCC(=O)OC[C@@H]1[C@H]([C@@H]([C@](O1)(CO)O)O)O
ACDLabs 12.01OC1(CO)C(O)C(O)C(COC(=O)CCCCCCC)O1
CACTVS 3.385CCCCCCCC(=O)OC[CH]1O[C](O)(CO)[CH](O)[CH]1O
FormulaC14 H26 O7
Name6-O-octanoyl-beta-D-fructofuranose
ChEMBL
DrugBank
ZINC
PDB chain3v8v Chain D Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3v8v Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA
Resolution2.6 Å
Binding residue
(original residue number in PDB)		R582 G588
Binding residue
(residue number reindexed from 1)		R552 G558
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.1.173: 23S rRNA (guanine(2445)-N(2))-methyltransferase.
2.1.1.264: 23S rRNA (guanine(2069)-N(7))-methyltransferase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008990 rRNA (guanine-N2-)-methyltransferase activity
GO:0052915 23S rRNA (guanine(2445)-N(2))-methyltransferase activity
GO:0070043 rRNA (guanine-N7-)-methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0070475 rRNA base methylation
GO:0070476 rRNA (guanine-N7)-methylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3v8v, PDBe:3v8v, PDBj:3v8v
PDBsum3v8v
PubMed22362734
UniProtP75864|RLMKL_ECOLI Ribosomal RNA large subunit methyltransferase K/L (Gene Name=rlmL)

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