Structure of PDB 5kk4 Chain D Binding Site BS02

Receptor Information

>5kk4 Chain D (length=47) Species: 157071 (Nicotiana suaveolens x Nicotiana tabacum)

KDCKRESNTFPGICITKPPCRKACIREKFTDGHCSKILRRCLCTKPC

Ligand information

• Ligand ID: 44E
• InChI: InChI=1S/C15H29O8P/c1-3-5-7-9-14(16)21-11-13(12-22-24(18,19)20)23-15(17)10-8-6-4-2/h13H,3-12H2,1-2H3,(H2,18,19,20)/t13-/m1/s1
• InChIKey: SFZZRGHNPILUOD-CYBMUJFWSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: CCCCCC(=O)OCC(COP(=O)(O)O)OC(=O)CCCCC
  CACTVS 3.385: CCCCCC(=O)OC[CH](CO[P](O)(O)=O)OC(=O)CCCCC
  CACTVS 3.385: CCCCCC(=O)OC[C@H](CO[P](O)(O)=O)OC(=O)CCCCC
  ACDLabs 12.01: O=C(OC(COP(=O)(O)O)COC(=O)CCCCC)CCCCC
  OpenEye OEToolkits 1.9.2: CCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCC
• Formula: C15 H29 O8 P
• Name: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate
• PDB chain: 5kk4 Chain D Residue 103

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5kk4 Binding of phosphatidic acid by NsD7 mediates the formation of helical defensin-lipid oligomeric assemblies and membrane permeabilization.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): I15 T16 K17 P18 H33 C34 K36 R39
• Binding residue (residue number reindexed from 1): I15 T16 K17 P18 H33 C34 K36 R39
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0008289 lipid binding
• GO:0070300 phosphatidic acid binding

Biological Process

• GO:0006952 defense response
• GO:0031640 killing of cells of another organism

Cellular Component

• GO:0005773 vacuole

External links

• PDB: RCSB:5kk4, PDBe:5kk4, PDBj:5kk4
• PDBsum: 5kk4
• PubMed: 27647905
• UniProt: C0HK49|DEF_NICSU Defensin NsD7