Structure of PDB 1kny Chain B Binding Site BS02

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 IDAPC
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKeyCAWZRIXWFRFUQB-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O12 P3
NameDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL132722
DrugBankDB02596
ZINCZINC000008295117
PDB chain1kny Chain B Residue 557 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1kny Structural investigation of the antibiotic and ATP-binding sites in kanamycin nucleotidyltransferase.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		S39 R42 S49 E52 T99 T187
Binding residue
(residue number reindexed from 1)		S39 R42 S49 E52 T99 T187
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)

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