Structure of PDB 8cue Chain 5M Binding Site BS01

Receptor Information

>8cue Chain 5M (length=70) Species: 176299 (Agrobacterium fabrum str. C58)

GGTDPATMVNNICTFILGPFGQSLAVLGIVAIGISWMFGRASLGLVAGVV
GGIVIMFGASFLGKTLTGGG

Ligand information

• Ligand ID: CPL
• InChI: InChI=1S/C42H80NO8P/c1-6-8-10-12-14-16-18-20-21-23-25-27-29-31-33-35-42(45)51-40(39-50-52(46,47)49-37-36-43(3,4)5)38-48-41(44)34-32-30-28-26-24-22-19-17-15-13-11-9-7-2/h14,16,20-21,40H,6-13,15,17-19,22-39H2,1-5H3/b16-14-,21-20-/t40-/m1/s1
• InChIKey: JLPULHDHAOZNQI-ZTIMHPMXSA-N
• SMILES:
  ACDLabs 10.04: O=C(OCC(OC(=O)CCCCCCC\C=C/C\C=C/CCCCC)COP([O-])(=O)OCC[N+](C)(C)C)CCCCCCCCCCCCCCC
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCCCCCC(=O)OCC(COP(=O)([O-])OCC[N+](C)(C)C)OC(=O)CCCCCCCC=CCC=CCCCCC
  CACTVS 3.341: CCCCCCCCCCCCCCCC(=O)OC[CH](CO[P]([O-])(=O)OCC[N+](C)(C)C)OC(=O)CCCCCCCC=CCC=CCCCCC
  CACTVS 3.341: CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P]([O-])(=O)OCC[N+](C)(C)C)OC(=O)CCCCCCC\C=C/C/C=C\CCCCC
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])OCC[N+](C)(C)C)OC(=O)CCCCCCC\C=C/C\C=C/CCCCC
• Formula: C42 H80 N O8 P
• Name: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE;
  PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE
• DrugBank: DB02306
• PDB chain: 8cue Chain 1L Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cue Cryo-EM structure of the Agrobacterium tumefaciens T-pilus reveals the importance of positive charges in the lumen.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): W87 L94 A98 V101
• Binding residue (residue number reindexed from 1): W36 L43 A47 V50
• Annotation score: 1

External links

• PDB: RCSB:8cue, PDBe:8cue, PDBj:8cue
• PDBsum: 8cue
• PubMed: 36513067
• UniProt: P17792|VIRB2_AGRFC Protein virB2 (Gene Name=virB2)