Structure of PDB 3p2k Chain A Binding Site BS01

Receptor Information
>3p2k Chain A (length=197) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFY
IGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSI
SILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTYKAYFLSEQYK
AELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHV
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 chain3p2k Chain A Residue 6735 [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]
PDB3p2k 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.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		G32 T33 N38 D55 P56 A87 E88 L104 F105 W107 L110 S195 W197
Binding residue
(residue number reindexed from 1)		G31 T32 N37 D54 P55 A86 E87 L103 F104 W106 L109 S176 W178
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=4.70,Kd=20uM
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:3p2k, PDBe:3p2k, PDBj:3p2k
PDBsum3p2k
PubMed21062819
UniProtA8C927|NPMA_ECOLX 16S rRNA (adenine(1408)-N(1))-methyltransferase (Gene Name=npmA)

[Back to BioLiP]