Structure of PDB 6s0s Chain E Binding Site BS02

Receptor Information
>6s0s Chain E (length=274) Species: 1967 (Streptomyces kanamyceticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LAAPPGELTLALTPDDKTLDPASLDRALAILAEHGILVLTGMLRTRLTDQ
LRTAMLDDLPEVLRQQDVPTNFVPGHVQQDPPVRESLLFPDVLLNPVVYQ
ITHAVLGADARNAVYSGNMNLPGSHEQPVHLDEPHLWPGISHPPYCLCVD
VPLIDFTLENGSTEYWPGSHVLNPDECYDERGCVLPAELERRRAVAPPVR
FPIPVGSVVIRDGRLWHRGVPNLSAAPRPLLAMTHYTEWFDMPPIQLPDT
VKSWVDGSDRHTHAHFVAGDVDHL
Ligand information
Ligand IDRIO
InChIInChI=1S/C17H34N4O10/c18-2-6-10(24)12(26)8(21)16(28-6)30-14-5(20)1-4(19)9(23)15(14)31-17-13(27)11(25)7(3-22)29-17/h4-17,22-27H,1-3,18-21H2/t4-,5+,6-,7-,8-,9+,10-,11-,12-,13-,14-,15-,16-,17+/m1/s1
InChIKeyNSKGQURZWSPSBC-VVPCINPTSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O(C2C(OC1OC(CN)C(O)C(O)C1N)C(N)CC(N)C2O)C3OC(C(O)C3O)CO
OpenEye OEToolkits 1.5.0C1C(C(C(C(C1N)OC2C(C(C(C(O2)CN)O)O)N)OC3C(C(C(O3)CO)O)O)O)N
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)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]3O)[CH](N)[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]2O[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)[C@H](N)[C@@H](O)[C@@H]1O
FormulaC17 H34 N4 O10
NameRIBOSTAMYCIN;
5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL;
(1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside
ChEMBLCHEMBL221572
DrugBankDB03615
ZINCZINC000053255716
PDB chain6s0s Chain E Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6s0s A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
N73 F74 V116 N120 H132 D134 E135 A234
Binding residue
(residue number reindexed from 1)
N71 F72 V114 N118 H130 D132 E133 A232
Annotation score4
Enzymatic activity
Enzyme Commision number 1.14.11.37: kanamycin B dioxygenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016706 2-oxoglutarate-dependent dioxygenase activity
Biological Process
GO:0017000 antibiotic biosynthetic process
GO:1901133 kanamycin biosynthetic process

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Molecular Function

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Biological Process
External links
PDB RCSB:6s0s, PDBe:6s0s, PDBj:6s0s
PDBsum6s0s
PubMed32592631
UniProtQ6L732|KANJ_STRKN Kanamycin B dioxygenase (Gene Name=kanJ)

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