Structure of PDB 3pb3 Chain A Binding Site BS01

Receptor Information
>3pb3 Chain A (length=199) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LILKGTKTVDLSKDELTEIIGQFDRVHIDMGTGDGRNIYKLAINDQNTFY
IGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESMPFELKNIADSI
SILFPWGTLLEYVIKPNRDILSNVADMAKKEAHFEFVTTYSDKAYFLSEQ
YKAELSNSGFRIDDVKELDNEYVKQFNSMWAKRLAFGRKRSFFRVSGHV
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 chain3pb3 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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PDB3pb3 Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G32 T33 N38 D55 P56 A86 A87 E88 L104 F105 W107 T109 L110 S195 W197
Binding residue
(residue number reindexed from 1)		G31 T32 N37 D54 P55 A85 A86 E87 L103 F104 W106 T108 L109 S178 W180
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=6.22,Kd=0.6uM
Enzymatic activity
Enzyme Commision number 2.1.1.180: 16S rRNA (adenine(1408)-N(1))-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
Biological Process
GO:0032259 methylation
GO:0046677 response to antibiotic

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3pb3, PDBe:3pb3, PDBj:3pb3
PDBsum3pb3
PubMed21062819
UniProtA8C927|NPMA_ECOLX 16S rRNA (adenine(1408)-N(1))-methyltransferase (Gene Name=npmA)

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