› 6b55

X-ray diffraction
2.5Å resolution

Crystal structure of the Plant Defensin NaD1 complexed with phosphatidic acid

Released:
DOI: 10.2210/pdb6b55/pdb
PDB entry 6b55 coloured by chain, front view.
PDB entry 6b55 coloured by chain, side view.
PDB entry 6b55 coloured by chain, top view.
Source organism: Nicotiana alata
Primary publication:
X-ray structure of a carpet-like antimicrobial defensin-phospholipid membrane disruption complex.
Järvå M, Lay FT, Phan TK, Humble C, Poon IKH, Bleackley MR, Anderson MA, Hulett MD, Kvansakul M
OpenAccess logo Nat Commun 9 1962 (2018)
PMID: 29773800

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo icosamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184576 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Flower-specific defensin Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Length: 48 amino acids
Theoretical weight: 5.39 KDa
Source organism: Nicotiana alata
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q8GTM0 (Residues: 25-72; Coverage: 59%)
Gene name: D1
Sequence domains: Gamma-thionin family
Structure domains: Knottin, scorpion toxin-like

Ligands and Environments

4 bound ligands:
Ligand PA8 14 x PA8
Ligand PO4 3 x PO4
Ligand PGE 5 x PGE
Ligand EDO 5 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: C2221
Unit cell:
a: 114.218Å b: 154.925Å c: 135.999Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.203 0.252
Expression system: Komagataella pastoris

Quick links

Citations

16 review citations

Plant antimicrobial peptides: structures, functions, and applications.
Li et al. (2021)
15 more

3 mentions without citation

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