Structure of PDB 8csf Chain B Binding Site BS03

Receptor Information

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

GLAVFLPPYPFRGLKAPYLWMFYKYLHCATDSILFITGEDYLSVTDAQRA
RWEFDPASMASLGYELPNAQSMACHEYLTLDNAFYETLLSRHHHDPIKSF
SAFLTERIPDLETELHALLDSKKGIIDQIDTFISICNCPSLEHVARTLGK
EVMHIEIGPLRAPMYRNTAYLDFAGVNGGTEASARYEKCQAEFDIKASLG
DLHNYFLEVLPPAEHSAAGVVLQVEDCSNLIAYNHDFTNISLLSYVRQRY
EKEDILVRAHPGSLFRLRDDVFTIDDSANSLAFINQCNEVFTINSSVGLE
AILTGKKTTVLGDCSYAFINELAGASATVNAAAFYLFSYLVPFDLVFNQE
YLKFRLGHPEEREIVGKHIEFYSADHSLSSLINEAISLEHH

Ligand information

• Ligand ID: KDO
• InChI: InChI=1S/C8H14O8/c9-2-4(11)6-5(12)3(10)1-8(15,16-6)7(13)14/h3-6,9-12,15H,1-2H2,(H,13,14)/t3-,4-,5-,6-,8-/m1/s1
• InChIKey: NNLZBVFSCVTSLA-HXUQBWEZSA-N
• SMILES:
  CACTVS 3.341: OC[C@@H](O)[C@H]1O[C@](O)(C[C@@H](O)[C@H]1O)C(O)=O
  OpenEye OEToolkits 1.5.0: C1[C@H]([C@H]([C@H](O[C@]1(C(=O)O)O)[C@@H](CO)O)O)O
  OpenEye OEToolkits 1.5.0: C1C(C(C(OC1(C(=O)O)O)C(CO)O)O)O
  CACTVS 3.341: OC[CH](O)[CH]1O[C](O)(C[CH](O)[CH]1O)C(O)=O
  ACDLabs 10.04: O=C(O)C1(O)OC(C(O)CO)C(O)C(O)C1
• Formula: C8 H14 O8
• Name: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid;
  3-deoxy-d-manno-oct-2-ulopyranosonic acid;
  2-keto-3-deoxy-D-mannooctanoic acid;
  3-deoxy-alpha-D-manno-oct-2-ulosonic acid;
  3-deoxy-D-manno-oct-2-ulosonic acid;
  3-deoxy-manno-oct-2-ulosonic acid
• DrugBank: DB03548
• ZINC: ZINC000005851513
• PDB chain: 8csf Chain B Residue 504

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): R163 N179 C232 S233
• Binding residue (residue number reindexed from 1): R161 N177 C227 S228
• Annotation score: 1

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