Structure of PDB 6f5w Chain A Binding Site BS03

Receptor Information

>6f5w Chain A (length=344) Species: 291112 (Photorhabdus asymbiotica)

TIALSEIVSVVNTSDGRLEVFGVGTDKAVWHNRQMAPHTGSPWSGWSSLK
GQVTSKPVVYINTDGRLEVFARGTDNALWHIWQTATNAGWSNWQSLGGVI
TSNPAIYANTDGRLEVFARGADNALWHISQTTAHSGPWSSWASLNGVITS
NPTVHINSDGRLEVFARGTDNALWHIWQTAPDSNLWSSWESLNGIITSDP
VVIDTADGRLEVFARGADNALWHIWQTISHSGPWSGWQSLNGVITSAPAV
AKNCDNRLEAFARGTDNALWHTWQTVSHSGPWSSWQSLNGVITSAPTAVR
DADGRLEVFARGTDNALWLTWQTASSWSPWISLGGVLIDASAIK

Ligand information

• Ligand ID: KG1
• InChI: InChI=1S/C9H14O5/c1-3-4-13-9-8(12)7(11)6(10)5(2)14-9/h4-12H,1H2,2H3/t5-,6+,7+,8-,9+/m0/s1
• InChIKey: ZGNQHYGPHWSZCN-JTPBWFLFSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC1C(C(C(C(O1)OC=C=C)O)O)O
  OpenEye OEToolkits 2.0.6: C[C@H]1[C@H]([C@H]([C@@H]([C@@H](O1)OC=C=C)O)O)O
  CACTVS 3.385: C[CH]1O[CH](O[CH]=[C]=[CH2])[CH](O)[CH](O)[CH]1O
  CACTVS 3.385: C[C@@H]1O[C@@H](O[CH]=[C]=[CH2])[C@@H](O)[C@H](O)[C@@H]1O
• Formula: C9 H14 O5
• Name: propadienyl 6-deoxy-alpha-L-galactopyranoside;
  propargyl-fucoside;
  propadienyl 6-deoxy-alpha-L-galactoside;
  propadienyl 6-deoxy-L-galactoside;
  propadienyl 6-deoxy-galactoside
• PDB chain: 6f5w Chain A Residue 415

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6f5w Synthesis of alpha-l-Fucopyranoside-Presenting Glycoclusters and Investigation of Their Interaction with Photorhabdus asymbiotica Lectin (PHL).
• Resolution: 1.91 Å
• Binding residue (original residue number in PDB): G267 V268 G289 T290 W295
• Binding residue (residue number reindexed from 1): G242 V243 G264 T265 W270
• Annotation score: 1
• Binding affinity: MOAD: Kd=149uM
  PDBbind-CN: -logKd/Ki=3.83,Kd=149uM

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:6f5w, PDBe:6f5w, PDBj:6f5w
• PDBsum: 6f5w
• PubMed: 29341313
• UniProt: C7BLE4