Structure of PDB 5vm8 Chain B Binding Site BS01

Receptor Information
>5vm8 Chain B (length=237) Species: 485 (Neisseria gonorrhoeae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMPRFYLPENLSVGQTVDLPDNIVRHLNVLRVRPNENITLFDGKGKAHTA
RLTVLEKHRAEAEILHEDTTDNESPLNITLIQSISSGDRMDFTLQKSVEL
GVTAIQPVISERCIVRAAKRLARWQEIVISACEQSGRNTVPPVLPIIGYR
EALDKMPSENTKLIMSINRACKLGDIRHPSGAIVFMVGPEGGWTEQEEQQ
AFEAGFQAVTLGKRILRTETAPLAAIAAMQTLWGDFT
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain5vm8 Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vm8 Crystal structure of a Ribosomal RNA small subunit methyltransferase E from Neisseria gonorrhoeae bound to S-adenosyl methionine
Resolution2.4 Å
Binding residue
(original residue number in PDB)		M169 G192 E194 G196 W197 L215 L220
Binding residue
(residue number reindexed from 1)		M165 G188 E190 G192 W193 L211 L216
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.193: 16S rRNA (uracil(1498)-N(3))-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0070042 rRNA (uridine-N3-)-methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0032259 methylation
GO:0070475 rRNA base 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:5vm8, PDBe:5vm8, PDBj:5vm8
PDBsum5vm8
PubMed
UniProtQ5F4Y3

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