› 4cqk

X-ray diffraction
1.6Å resolution

Crystal structure of ligand-bound NaD1

Released:
DOI: 10.2210/pdb4cqk/pdb
PDB entry 4cqk coloured by chain, front view.
PDB entry 4cqk coloured by chain, side view.
PDB entry 4cqk coloured by chain, top view.
Source organism: Nicotiana alata
Primary publication:
Phosphoinositide-mediated oligomerization of a defensin induces cell lysis.
Poon IKh, Baxter AA, Lay FT, Mills GD, Adda CG, Payne JA, Phan TK, Ryan GF, White JA, Veneer PK, van der Weerden NL, Anderson MA, Kvansakul M, Hulett MD
Elife 3 e01808 (2014)
PMID: 24692446

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184575 (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
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N
Length: 47 amino acids
Theoretical weight: 5.32 KDa
Source organism: Nicotiana alata
UniProt:
  • Canonical: Q8GTM0 (Residues: 26-72; Coverage: 59%)
Gene name: D1
Sequence domains: Gamma-thionin family
Structure domains: Knottin, scorpion toxin-like

Ligands and Environments

3 bound ligands:
Ligand PIO 14 x PIO
Ligand SO4 20 x SO4
Ligand MRD 4 x MRD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: C2221
Unit cell:
a: 79.64Å b: 132.04Å c: 153.01Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.156 0.155 0.184

Quick links

Citations

24 review citations

Neutrophil extracellular traps in immunity and disease.
Papayannopoulos V. (2018)
23 more

8 mentions without citation

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