Structure of PDB 6p08 Chain D Binding Site BS04

Receptor Information

>6p08 Chain D (length=252) Species: 1409 (Bacillus sp. (in: firmicutes))

NGPIIMTREERMKIVHEIKERILDKYGDDVKAIGVYGSLGRQTDGPYSDI
DMMCVMSTEEAEFSHEWTTGEWKVEVNFDSEEILLDYASQVESDWPLTHG
QFFSILPIYDSGGYLEKVYQTAKSVEAQKFHDAICALIVEELFEYAGKWR
NIRVQGPTTFLPSLTVQVAMAGAMLIGLHHRICYTTSASVLTEAVKQSDL
PSGYDHLCQFVMSGQLSDSEKLLESLENFWNGIQEWTERHGYIVDVSKRI
PF

Ligand information

• Ligand ID: NMY
• InChI: InChI=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
• InChIKey: PGBHMTALBVVCIT-VCIWKGPPSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1C(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 3.341: NC[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 1.5.0: C1[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 3.341: NC[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 10.04: O(C2C(OC1OC(CN)C(O)C(O)C1N)C(N)CC(N)C2O)C4OC(C(OC3OC(CN)C(O)C(O)C3N)C4O)CO
• Formula: C23 H46 N6 O13
• Name: NEOMYCIN;
  MYCIFRADIN;
  NEOMAS;
  PIMAVECORT;
  VONAMYCIN
• ChEMBL: CHEMBL184618
• DrugBank: DB00452
• ZINC: ZINC000071928291
• PDB chain: 6p08 Chain A Residue 307

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6p08 Catch and Release": a Variation of the Archetypal Nucleotidyl Transfer Reaction
• Resolution: 2.27 Å
• Binding residue (original residue number in PDB): Y37 D52 E63 E67 E76 D80 Y88 Q102
• Binding residue (residue number reindexed from 1): Y36 D51 E62 E66 E75 D79 Y87 Q101
• Annotation score: 1

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

External links

• PDB: RCSB:6p08, PDBe:6p08, PDBj:6p08
• PDBsum: 6p08
• UniProt: P05058|KANU_BACSP Kanamycin nucleotidyltransferase (Gene Name=knt)