Structure of PDB 1qaq Chain A Binding Site BS01

Receptor Information
>1qaq Chain A (length=236) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAI
EIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNIST
DIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSLALFLMAEVDISILSMV
PREYFHPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFT
KNQFNNSLKHAGIDDLNNISFEQFLSLFNSYKLFNK
Ligand information
Ligand IDSFG
InChIInChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
InChIKeyLMXOHSDXUQEUSF-YECHIGJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
CACTVS 3.370N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N7 O5
NameSINEFUNGIN;
ADENOSYL-ORNITHINE
ChEMBLCHEMBL1214186
DrugBankDB01910
ZINCZINC000004217451
PDB chain1qaq Chain A Residue 245 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1qaq The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		Q10 N11 F12 I13 G38 S39 G40 E59 I60 L64 D84 I85 N101 P103 I106
Binding residue
(residue number reindexed from 1)		Q2 N3 F4 I5 G30 S31 G32 E51 I52 L56 D76 I77 N93 P95 I98
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=4.74,Ki=18uM
Enzymatic activity
Catalytic site (original residue number in PDB) G38 E59 N101 Y104 F163
Catalytic site (residue number reindexed from 1) G30 E51 N93 Y96 F155
Enzyme Commision number 2.1.1.184: 23S rRNA (adenine(2085)-N(6))-dimethyltransferase.
Gene Ontology
Molecular Function
GO:0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity
GO:0003723 RNA binding
GO:0008168 methyltransferase activity
GO:0052910 23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity
Biological Process
GO:0000154 rRNA modification
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0046677 response to antibiotic
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1qaq, PDBe:1qaq, PDBj:1qaq
PDBsum1qaq
PubMed10366505
UniProtP13956|ERM_BACIU rRNA adenine N-6-methyltransferase (Gene Name=ermC')

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