Structure of PDB 3lcu Chain A Binding Site BS01

Receptor Information
>3lcu Chain A (length=260) 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
GNELIYVIQK
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain3lcu Chain A Residue 6732 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3lcu 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.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		I60 F64 H102 S104 T105 R108 A133 C134 D156 I157 D182 L183 L198 Q207
Binding residue
(residue number reindexed from 1)		I53 F57 H95 S97 T98 R101 A126 C127 D149 I150 D175 L176 L191 Q200
Annotation score5
Binding affinityMOAD: Kd=300uM
PDBbind-CN: -logKd/Ki=3.52,Kd=300uM
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:3lcu, PDBe:3lcu, PDBj:3lcu
PDBsum3lcu
PubMed20194115
UniProtQ7M0R2|SGM_MICZI 16S rRNA (guanine(1405)-N(7))-methyltransferase (Gene Name=sgm)

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