› 5vyp

X-ray diffraction
2.6Å resolution

Crystal structure of the Plant Defensin NsD7 bound to PIP2

Released:
DOI: 10.2210/pdb5vyp/pdb
PDB entry 5vyp coloured by chain, front view.
PDB entry 5vyp coloured by chain, side view.
PDB entry 5vyp coloured by chain, top view.
Source organism: Nicotiana suaveolens
Primary publication:
Structure of the defensin NsD7 in complex with PIP2 reveals that defensin:lipid oligomer topologies are dependent on lipid type.
Jarva M, Lay FT, Hulett MD, Kvansakul M
FEBS Lett. (2017)
PMID: 28741756

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo 24-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110957 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Defensin NsD7 Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
Length: 48 amino acids
Theoretical weight: 5.47 KDa
Source organism: Nicotiana suaveolens
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

3 bound ligands:
Ligand PIO 24 x PIO
Ligand SO4 8 x SO4
Ligand GOL 12 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P21
Unit cell:
a: 75.605Å b: 83.489Å c: 105.194Å
α: 90° β: 93.99° γ: 90°
R-values:
R R work R free
0.217 0.214 0.27
Expression system: Komagataella pastoris

Quick links

Citations

2 review citations

Membrane-Interacting Antifungal Peptides.
Struyfs et al. (2021)
1 more

2 mentions without citation

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