Structure of PDB 6rgr Chain A Binding Site BS01

Receptor Information

>6rgr Chain A (length=341) Species: 291112 (Photorhabdus asymbiotica)

TIALSEIVSVVNTSDGRLEVFGVGTDKAVWHNRQMAPHTGSPWSGWSSLK
GQVTSKPVVYINTDGRLEVFARGTDNALWHIWQTATNAGWSNWQSLGGVI
TSNPAIYANTDGRLEVFARGADNALWHISQTTAHSGPWSSWASLNGVITS
NPTVHINSDGRLEVFARGTDNALWHIWQTAPDSNLWSSWESLNGIITSDP
VVIDTADGRLEVFARGADNALWHIWQTSGPWSGWQSLNGVITSAPAVAKN
CDNRLEAFARGTDNALWHTWQTVSHSGPWSSWQSLNGVITSAPTAVRDAD
GRLEVFARGTDNALWLTWQTASSWSPWISLGGVLIDASAIK

Ligand information

• Ligand ID: RM4
• InChI: InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6-/m0/s1
• InChIKey: SHZGCJCMOBCMKK-YJRYQGEOSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O)O)O)O
  CACTVS 3.341: C[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)C
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)O)O)O)O
  CACTVS 3.341: C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
• Formula: C6 H12 O5
• Name: beta-L-rhamnopyranose;
  beta-L-rhamnose;
  6-deoxy-beta-L-mannopyranose;
  L-rhamnose;
  rhamnose
• ZINC: ZINC000003861281
• PDB chain: 6rgr Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6rgr Heptabladed beta-propeller lectins PLL2 and PHL from Photorhabdus spp. recognize O-methylated sugars and influence the host immune system.
• Resolution: 1.89 Å
• Binding residue (original residue number in PDB): R186 E188 H200 W202 Q251 G257 W259
• Binding residue (residue number reindexed from 1): R161 E163 H175 W177 Q226 G229 W231
• Annotation score: 4
• Binding affinity: MOAD: ic50=147mM

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:6rgr, PDBe:6rgr, PDBj:6rgr
• PDBsum: 6rgr
• PubMed: 32559333
• UniProt: C7BLE4