› 5kk4

X-ray diffraction
1.7Å resolution

Crystal Structure of the Plant Defensin NsD7 bound to Phosphatidic Acid

Released:
DOI: 10.2210/pdb5kk4/pdb
PDB entry 5kk4 coloured by chain, front view.
PDB entry 5kk4 coloured by chain, side view.
PDB entry 5kk4 coloured by chain, top view.
Source organism: Nicotiana suaveolens x Nicotiana tabacum
Primary publication:
Binding of phosphatidic acid by NsD7 mediates the formation of helical defensin-lipid oligomeric assemblies and membrane permeabilization.
Kvansakul M, Lay FT, Adda CG, Veneer PK, Baxter AA, Phan TK, Poon IK, Hulett MD
Proc Natl Acad Sci U S A 113 11202-11207 (2016)
PMID: 27647905

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110958 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Defensin NsD7 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 48 amino acids
Theoretical weight: 5.47 KDa
Source organism: Nicotiana suaveolens x Nicotiana tabacum
Expression system: Komagataella pastoris
UniProt:
  • Canonical: C0HK49 (Residues: 1-47; Coverage: 100%)
Sequence domains: Gamma-thionin family
Structure domains: Knottin, scorpion toxin-like

Ligands and Environments

4 bound ligands:
Ligand EDO 17 x EDO
Ligand SO4 5 x SO4
Ligand ACT 3 x ACT
Ligand 44E 6 x 44E
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: C2
Unit cell:
a: 107.47Å b: 62.327Å c: 53.644Å
α: 90° β: 118.69° γ: 90°
R-values:
R R work R free
0.185 0.183 0.212
Expression system: Komagataella pastoris

Quick links

Citations

8 review citations

Tumor cell membrane-targeting cationic antimicrobial peptides: novel insights into mechanisms of action and therapeutic prospects.
Baxter et al. (2017)
7 more

4 mentions without citation

Plant Defensins from a Structural Perspective.
Kovaleva et al. (2020)
3 more