Structure of PDB 3v8v Chain B Binding Site BS05

Receptor Information
>3v8v Chain B (length=636) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNSLFASTARGLEELLKTELENLGAVECQVVQGGVHFKGDTRLVYQSLMW
SRLASRIMLPLGECYSDLDLYLGVQAINWTEMFNPGATFAVHRNSQYGAM
KVKDAIVDAFTRPRPNVDRDAPDIRVNVWIALDLSGDGLHLRGYRDAPIK
ETLAAAIVMRSGWQPGTPLLDPMCGSGTLLIEAAMLATDRAPGLHRGRWG
FSGWAQHDEAIWQEVKAEAQTRARKGLAEYSSHFYGSDSDARVIQRARTN
ARLAGIGELITFEVKDVAQLTNPLPKGPYGTVLSNPPYSEPALIALHSLL
GRIMKNQFGGWNLSLFSASPDLLSCLQLRADKQYKAKNGPLDCVQKNYHV
AESEDYTNRLRKNLKKFEKWARQEGIECYRLYDADLPEYNVAVDRYADWV
VVQEYAHKARQRLFDIIAATISVLGIAPNKLVLKTRKGEFLEVTEYNAHL
WVNLTDYLDTGLFLDHRIARRMLGQMSKGKDFLNLFSYTGSATVHAGLGG
ARSTTTVDMSRTYLEWAERNLRLNGLTGRAHRLIQADCLAWLREANEQFD
LIFIDPPTFSNAFDVQRDHLALMKDLKRLLRAGGTIMFSNNKRGFRMDLD
GLAKLGLKAQEITQKTLSQDFARNRQIHNCWLITAA
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 chain3v8v Chain B Residue 802 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		F546 Y548 D568 M569 D597 C598 D615 S620
Binding residue
(residue number reindexed from 1)		F486 Y488 D508 M509 D537 C538 D555 S560
Annotation score5
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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