Structure of PDB 5cx8 Chain A Binding Site BS01

Receptor Information

>5cx8 Chain A (length=472) Species: 242619 (Porphyromonas gingivalis W83)

DFQQPYTSFVQTKQNRDGLYALLRNTENPRMHFYQELQSDMYCTTITDGN
SLAPFVNWDLGILNDHGRADEDEVSGIAGYYFVYNRLNQQANAFVNNTEA
ALQNQVYKNSTEIANAKSFLAEGKVLQALAIWRLMDRFSFHESVTEVNSG
AKDLGVILLKEYNPGYIGPRATKAQCYDYILSRLSEAIEVLPENRESVLY
VSRDYAYALRARIYLALGEYGKAAADAKMVVDKYPLIGAADASEFENIYR
SDANNPEIIFRGFASATLGSFTATTLNGAAPAGKDIKYNPSAVPFQWVVD
LYENEDFRKSVYIAKVVKKDKGYLVNKFLEDKAYRDVQDKPNLKVGARYF
SVAEVYLILVESALQTGDTPTAEKYLKALSKARGAEVSVVNMEALQAERT
RELIGEGSRLRDMVRWSIPNNHDAFETQPGLEGFANTTPLKAQAPVGFYA
YTWEFPQRDRQTNPQLIKNWPI

Ligand information

• Ligand ID: 3DO
• InChI: InChI=1S/C6H12O5/c7-2-5-3(8)1-4(9)6(10)11-5/h3-10H,1-2H2/t3-,4+,5+,6+/m0/s1
• InChIKey: RJDIFQMDPPUATQ-SLPGGIOYSA-N
• SMILES:
  CACTVS 3.385: OC[CH]1O[CH](O)[CH](O)C[CH]1O
  CACTVS 3.385: OC[C@H]1O[C@@H](O)[C@H](O)C[C@@H]1O
  ACDLabs 12.01: OC1C(OC(O)C(O)C1)CO
  OpenEye OEToolkits 1.7.6: C1C(C(OC(C1O)O)CO)O
  OpenEye OEToolkits 1.7.6: C1[C@@H]([C@H](O[C@H]([C@@H]1O)O)CO)O
• Formula: C6 H12 O5
• Name: 3-deoxy-beta-D-glucopyranose;
  3-deoxy-beta-D-ribo-hexopyranose;
  3-deoxy-beta-D-glucose;
  3-deoxy-D-glucose;
  3-deoxy-glucose
• ZINC: ZINC000013547141
• PDB chain: 5cx8 Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5cx8 Structure of RagB, a major immunodominant outer-membrane surface receptor antigen of Porphyromonas gingivalis.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): D329 L330 E332
• Binding residue (residue number reindexed from 1): D300 L301 E303
• Annotation score: 1

Gene Ontology

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:5cx8, PDBe:5cx8, PDBj:5cx8
• PDBsum: 5cx8
• PubMed: 26441291
• UniProt: F5H948