Structure of PDB 5mxf Chain A Binding Site BS01

Receptor Information

>5mxf Chain A (length=346) Species: 553480 (Photorhabdus asymbiotica subsp. asymbiotica ATCC 43949)

MSTIALSEIVSVVNTSDGRLEVFGVGTDKAVWHNRQMAPHTGSPWSGWSS
LKGQVTSKPVVYINTDGRLEVFARGTDNALWHIWQTATNAGWSNWQSLGG
VITSNPAIYANTDGRLEVFARGADNALWHISQTTAHSGPWSSWASLNGVI
TSNPTVHINSDGRLEVFARGTDNALWHIWQTAPDSNLWSSWESLNGIITS
DPVVIDTADGRLEVFARGADNALWHIWQTISHSGPWSGWQSLNGVITSAP
AVAKNCDNRLEAFARGTDNALWHTWQTVSHSGPWSSWQSLNGVITSAPTA
VRDADGRLEVFARGTDNALWLTWQTASSWSPWISLGGVLIDASAIK

Ligand information

• Ligand ID: MFU
• InChI: InChI=1S/C7H14O5/c1-3-4(8)5(9)6(10)7(11-2)12-3/h3-10H,1-2H3/t3-,4+,5+,6-,7+/m0/s1
• InChIKey: OHWCAVRRXKJCRB-CXNFULCWSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)OC)O)O)O
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@H]([C@H]([C@@H]([C@@H](O1)OC)O)O)O
  ACDLabs 10.04: OC1C(O)C(O)C(OC1OC)C
  CACTVS 3.341: CO[CH]1O[CH](C)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: CO[C@@H]1O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]1O
• Formula: C7 H14 O5
• Name: methyl alpha-L-fucopyranoside;
  ALPHA-L-METHYL-FUCOSE;
  methyl 6-deoxy-alpha-L-galactopyranoside;
  methyl alpha-L-fucoside;
  methyl L-fucoside;
  methyl fucoside
• ChEMBL: CHEMBL1234282
• DrugBank: DB03879
• ZINC: ZINC000002509839
• PDB chain: 5mxf Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mxf Characterization of novel bangle lectin from Photorhabdus asymbiotica with dual sugar-binding specificity and its effect on host immunity.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): G315 V316 G337 T338 W343
• Binding residue (residue number reindexed from 1): G292 V293 G314 T315 W320
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.26mM
  PDBbind-CN: -logKd/Ki=3.59,Kd=0.26mM

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:5mxf, PDBe:5mxf, PDBj:5mxf
• PDBsum: 5mxf
• PubMed: 28806750
• UniProt: C7BLE4