Structure of PDB 6p06 Chain A Binding Site BS01

Receptor Information
>6p06 Chain A (length=253) Species: 1409 (Bacillus sp. (in: firmicutes)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNGPIIMTREERMKIVHEIKERILDKYGDDVKAIGVYGSLGRQTDGPYSD
IDMMCVMSTEEAEFSHEWTTGEWKVEVNFDSEEILLDYASQVESDWPLTH
GQFFSILPIYDSGGYLEKVYQTAKSVEAQKFHDAICALIVEELFEYAGKW
RNIRVQGPTTFLPSLTVQVAMAGAMLIGLHHRICYTTSASVLTEAVKQSD
LPSGYDHLCQFVMSGQLSDSEKLLESLENFWNGIQEWTERHGYIVDVSKR
IPF
Ligand information
Ligand IDNMY
InChIInChI=1S/C23H46N6O13/c24-2-7-13(32)15(34)10(28)21(37-7)40-18-6(27)1-5(26)12(31)20(18)42-23-17(36)19(9(4-30)39-23)41-22-11(29)16(35)14(33)8(3-25)38-22/h5-23,30-36H,1-4,24-29H2/t5-,6+,7-,8+,9-,10-,11-,12+,13-,14-,15-,16-,17-,18-,19-,20-,21-,22-,23+/m1/s1
InChIKeyPGBHMTALBVVCIT-VCIWKGPPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(C(C(C(C1N)OC2C(C(C(C(O2)CN)O)O)N)OC3C(C(C(O3)CO)OC4C(C(C(C(O4)CN)O)O)N)O)O)N
CACTVS 3.341NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O)[CH]2O[CH]3O[CH](CO)[CH](O[CH]4O[CH](CN)[CH](O)[CH](O)[CH]4N)[CH]3O)[CH](N)[CH](O)[CH]1O
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)N)O[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O[C@@H]4[C@@H]([C@H]([C@@H]([C@@H](O4)CN)O)O)N)O)O)N
CACTVS 3.341NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O[C@@H]3O[C@H](CO)[C@@H](O[C@H]4O[C@@H](CN)[C@@H](O)[C@H](O)[C@H]4N)[C@H]3O)[C@H](N)[C@@H](O)[C@@H]1O
ACDLabs 10.04O(C2C(OC1OC(CN)C(O)C(O)C1N)C(N)CC(N)C2O)C4OC(C(OC3OC(CN)C(O)C(O)C3N)C4O)CO
FormulaC23 H46 N6 O13
NameNEOMYCIN;
MYCIFRADIN;
NEOMAS;
PIMAVECORT;
VONAMYCIN
ChEMBLCHEMBL184618
DrugBankDB00452
ZINCZINC000071928291
PDB chain6p06 Chain A Residue 301 [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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PDB6p06 Catch and Release": a Variation of the Archetypal Nucleotidyl Transfer Reaction
Resolution2.3 Å
Binding residue
(original residue number in PDB)
Y37 D52 E67 E76 D80 Y88 Q102
Binding residue
(residue number reindexed from 1)
Y37 D52 E67 E76 D80 Y88 Q102
Annotation score1
Enzymatic activity
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

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Molecular Function

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Biological Process
External links
PDB RCSB:6p06, PDBe:6p06, PDBj:6p06
PDBsum6p06
PubMed
UniProtP05058|KANU_BACSP Kanamycin nucleotidyltransferase (Gene Name=knt)

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