Structure of PDB 3rfa Chain A Binding Site BS02

Receptor Information
>3rfa Chain A (length=333) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KINLLDLNRQQMREFFKDLGEKPFRADQVMKWMYHYCCDNFDEMTDINKV
LRGKLKEVAEIRAPEVVEEQRSSDGTIKWAIAVGDQRVETVYIPEDDRAT
LCVSSQVGCALECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIVGAAKVTG
QRPITNVVMMGMGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVV
PALDKLGDMIDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLE
KSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKDTPCKINLIPWNPFPG
APYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGD
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 chain3rfa Chain A Residue 406 [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]
PDB3rfa Structural basis for methyl transfer by a radical SAM enzyme.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		F131 C132 M176 G177 G179 E180 S211 T212 S233 H235 V280 I309 W311 N312
Binding residue
(residue number reindexed from 1)		F115 C116 M160 G161 G163 E164 S195 T196 S217 H219 V264 I293 W295 N296
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E105 C118 C125 C129 C132
Catalytic site (residue number reindexed from 1) E89 C102 C109 C113 C116
Enzyme Commision number 2.1.1.192: 23S rRNA (adenine(2503)-C(2))-methyltransferase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0002935 tRNA (adenine(37)-C2)-methyltransferase activity
GO:0003824 catalytic activity
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0019843 rRNA binding
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0070040 rRNA (adenine(2503)-C2-)-methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation
GO:0046677 response to antibiotic
GO:0070475 rRNA base methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3rfa, PDBe:3rfa, PDBj:3rfa
PDBsum3rfa
PubMed21527678
UniProtP36979|RLMN_ECOLI Dual-specificity RNA methyltransferase RlmN (Gene Name=rlmN)

[Back to BioLiP]