Structure of PDB 3lcv Chain B Binding Site BS01

Receptor Information
>3lcv Chain B (length=259) Species: 1879 (Micromonospora zionensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DRIDEIERAITKSRRYQTVAPATVRRLARAALVAARGDVPDAVKRTKRGL
HEIYGAFLPPSPPNYAALLRHLDSAVDAGDDEAVRAALLRAMSVHISTRE
RLPHLDEFYRELFRHLPRPNTLRDLACGLNPLAAPWMGLPAETVYIASDI
DARLVGFVDEALTRLNVPHRTNVADLLEDRLDEPADVTLLLKTLPCLETQ
QRGSGWEVIDIVNSPNIVVTFPTKGMFQNYSQSFESQARERSCRIQRLEI
GNELIYVIQ
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 chain3lcv Chain B Residue 301 [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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PDB3lcv Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		I60 F64 S104 T105 R108 A133 C134 D156 I157 D182 L183 L198 K199 Q207
Binding residue
(residue number reindexed from 1)		I53 F57 S97 T98 R101 A126 C127 D149 I150 D175 L176 L191 K192 Q200
Annotation score5
Binding affinityMOAD: Kd=18uM
PDBbind-CN: -logKd/Ki=4.74,Kd=18uM
Enzymatic activity
Enzyme Commision number 2.1.1.179: 16S rRNA (guanine(1405)-N(7))-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0008649 rRNA methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0046677 response to antibiotic

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3lcv, PDBe:3lcv, PDBj:3lcv
PDBsum3lcv
PubMed20194115
UniProtQ7M0R2|SGM_MICZI 16S rRNA (guanine(1405)-N(7))-methyltransferase (Gene Name=sgm)

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