Structure of PDB 8kif Chain D Binding Site BS02

Receptor Information

>8kif Chain D (length=282) Species: 216594 (Mycobacterium marinum M)

NVKGEGLGAQITGVDPKNLDDITTDEIRDIVYANKLVILKDVNPSPEEFL
KLGKIVGQIVPYYEPMYHHEDHPEIFVSSTEEGQGVPKTGAFWHIDYMFM
PEPFAFSMVLPLAVPGHDRGTYFIDLAKVWASLPAAQQAPARGTLSTHDP
RRHIKIRPSDVYRPIGEVWDEISRATPPIKWPTVIRHPKTGEEILYICAT
GTTKIDNLVDPAVLAELLAATGQLDPEYNSPFIHTQHYEVGDIILWDNRV
LMHRAKHGTASGTLTTYRLTMLDGLETPGYPA

Ligand information

• Ligand ID: VY9
• InChI: InChI=1S/C12H23NO4/c1-2-3-4-5-6-7-10(8-11(14)15)13-9-12(16)17/h10,13H,2-9H2,1H3,(H,14,15)(H,16,17)
• InChIKey: DKLSSPDDVJYWNG-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: CCCCCCC[C@@H](CC(O)=O)NCC(O)=O
  CACTVS 3.385: CCCCCCC[CH](CC(O)=O)NCC(O)=O
  OpenEye OEToolkits 2.0.7: CCCCCCCC(CC(=O)O)NCC(=O)O
  OpenEye OEToolkits 2.0.7: CCCCCCC[C@H](CC(=O)O)NCC(=O)O
• Formula: C12 H23 N O4
• Name: (3R)-3-(2-hydroxy-2-oxoethylamino)decanoic acid
• PDB chain: 8kif Chain D Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8kif Variation in Biosynthesis and Metal-Binding Properties of Isonitrile-Containing Peptides Produced by Mycobacteria versus Streptomyces
• Resolution: 2.13 Å
• Binding residue (original residue number in PDB): Y81 Y86 T108 G109 F111 D115 Y116 F118 P169 K174 T219 R291
• Binding residue (residue number reindexed from 1): Y62 Y67 T89 G90 F92 D96 Y97 F99 P150 K155 T200 R268
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

External links

• PDB: RCSB:8kif, PDBe:8kif, PDBj:8kif
• PDBsum: 8kif
• PubMed: 38895101
• UniProt: B2HKM3|INLPE_MYCMM (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase (Gene Name=mmaE)