Structure of PDB 8csf Chain B Binding Site BS01

Receptor Information

>8csf Chain B (length=391) Species: 577 (Raoultella terrigena)

GLAVFLPPYPFRGLKAPYLWMFYKYLHCATDSILFITGEDYLSVTDAQRA
RWEFDPASMASLGYELPNAQSMACHEYLTLDNAFYETLLSRHHHDPIKSF
SAFLTERIPDLETELHALLDSKKGIIDQIDTFISICNCPSLEHVARTLGK
EVMHIEIGPLRAPMYRNTAYLDFAGVNGGTEASARYEKCQAEFDIKASLG
DLHNYFLEVLPPAEHSAAGVVLQVEDCSNLIAYNHDFTNISLLSYVRQRY
EKEDILVRAHPGSLFRLRDDVFTIDDSANSLAFINQCNEVFTINSSVGLE
AILTGKKTTVLGDCSYAFINELAGASATVNAAAFYLFSYLVPFDLVFNQE
YLKFRLGHPEEREIVGKHIEFYSADHSLSSLINEAISLEHH

Ligand information

• Ligand ID: RAM
• 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-HGVZOGFYSA-N
• SMILES:
  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: C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O)O)O)O
  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: alpha-L-rhamnopyranose;
  alpha-L-rhamnose;
  6-deoxy-alpha-L-mannopyranose;
  L-rhamnose;
  rhamnose
• ZINC: ZINC000003861280
• PDB chain: 8csf Chain F Residue 2

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8csf The retaining beta-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): R12 Y18 W20 E158
• Binding residue (residue number reindexed from 1): R12 Y18 W20 E156
• Annotation score: 4

Gene Ontology

Biological Process

• GO:0000271 polysaccharide biosynthetic process
• GO:0015774 polysaccharide transport

External links

• PDB: RCSB:8csf, PDBe:8csf, PDBj:8csf
• PDBsum: 8csf
• PubMed: 36271007
• UniProt: Q6U8B0