Structure of PDB 1kny Chain B Binding Site BS03

Receptor Information
>1kny Chain B (length=253) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNGPIIMTREERMKIVHEIKERILDKYGDDVKAIGVYGSLGRQTDGPYSD
IEMMCVMSTEEAEFSHEWTTGEWKVEVNFYSEEILLDYASQVESDWPLTH
GQFFSILPIYDSGGYLEKVYQTAKSVEAQTFHDAICALIVEELFEYAGKW
RNIRVQGPTTFLPSLTVQVAMAGAMLIGLHHRICYTTSASVLTEAVKQSD
LPSGYDHLCQFVMSGQLSDSEKLLESLENFWNGIQEWTERHGYIVDVSKR
IPF
Ligand information
Ligand IDKAN
InChIInChI=1S/C18H36N4O11/c19-2-6-10(25)12(27)13(28)18(30-6)33-16-5(21)1-4(20)15(14(16)29)32-17-11(26)8(22)9(24)7(3-23)31-17/h4-18,23-29H,1-3,19-22H2/t4-,5+,6-,7-,8+,9-,10-,11-,12+,13-,14-,15+,16-,17-,18-/m1/s1
InChIKeySBUJHOSQTJFQJX-NOAMYHISSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O)[CH]2O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O
ACDLabs 10.04O(C2C(O)C(OC1OC(CN)C(O)C(O)C1O)C(N)CC2N)C3OC(C(O)C(N)C3O)CO
OpenEye OEToolkits 1.5.0C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CN)O)O)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)N)O)N
OpenEye OEToolkits 1.5.0C1C(C(C(C(C1N)OC2C(C(C(C(O2)CN)O)O)O)O)OC3C(C(C(C(O3)CO)O)N)O)N
FormulaC18 H36 N4 O11
NameKANAMYCIN A
ChEMBLCHEMBL1384
DrugBankDB01172
ZINCZINC000008214590
PDB chain1kny Chain B Residue 559 [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]
PDB1kny Structural investigation of the antibiotic and ATP-binding sites in kanamycin nucleotidyltransferase.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		S94 D95 E141 E145
Binding residue
(residue number reindexed from 1)		S94 D95 E141 E145
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D50 E52 E145 K149
Catalytic site (residue number reindexed from 1) D50 E52 E145 K149
Enzyme Commision number 2.7.7.-
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
Biological Process
GO:0046677 response to antibiotic

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1kny, PDBe:1kny, PDBj:1kny
PDBsum1kny
PubMed7577914
UniProtP05057|KANU_STAAU Kanamycin nucleotidyltransferase (Gene Name=knt)

[Back to BioLiP]