Structure of PDB 8csd Chain A Binding Site BS01

Receptor Information

>8csd Chain A (length=397) Species: 577 (Raoultella terrigena)

GLAVFLPPYPFRGLKAPYLWMFYKYLHCATDSILFITGEDYLSVTDDEAQ
RARWEFDPASMASLGYELPNAQSMACHEYLTLDNAFYETLLSRHHHDPIK
SFSAFLTERIPDLETELHALLDSKKGIIDQIDTFISICNCPSLEHVARTL
GKEVMHIEIGPLRAPMYRNTAYLDFAGVNGGTEASARYEKCQAEFDIKAS
LGDLHNYFLEVLPPAETHSAAGVVLQVEDCSNLIAYNHDFTNISLLSYVR
QRYEKEDILVRAHPGSLFRLRDDVFTIDDSANSLAFINQCNEVFTINSSV
GLEAILTGKKTTVLGDCSYAFINELAGASATVNAAAFYLFSYLVPFDLVF
NQEYLKFRLGHPEEREIVGKHIEFYSADMPHSLSSLINEAISLEHHH

Ligand information

• Ligand ID: C5P
• InChI: InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: IERHLVCPSMICTF-XVFCMESISA-N
• SMILES:
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
  ACDLabs 10.04: O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
• Formula: C9 H14 N3 O8 P
• Name: CYTIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL307679
• DrugBank: DB03403
• ZINC: ZINC000003861744
• PDB chain: 8csd Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8csd The retaining beta-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): R163 L227 R263 A264 H265 P266 S285 S300 S301 V302
• Binding residue (residue number reindexed from 1): R163 L225 R261 A262 H263 P264 S283 S298 S299 V300
• Annotation score: 4

Gene Ontology

Biological Process

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

External links

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