› 1zmk

X-ray diffraction
1.3Å resolution

Crystal structure of human alpha-defensin-2 (variant Gly16-> D-ALA), P 42 21 2 space group

Released:
DOI: 10.2210/pdb1zmk/pdb
PDB entry 1zmk coloured by chain, front view.
PDB entry 1zmk coloured by chain, side view.
PDB entry 1zmk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Reconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids.
Xie C, Prahl A, Ericksen B, Wu Z, Zeng P, Li X, Lu WY, Lubkowski J, Lu W
J Biol Chem 280 32921-9 (2005)
PMID: 15894545

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo octamer
Assembly name:
PDBe Complex ID:
PDB-CPX-157841 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Neutrophil defensin 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 29 amino acids
Theoretical weight: 3.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P59666 (Residues: 66-94; Coverage: 39%)
Gene names: DEF3, DEFA3
Sequence domains: Mammalian defensin

Ligands and Environments

2 bound ligands:
Ligand CL 2 x CL
Ligand GOL 1 x GOL
1 modified residue:
Ligand DAL 2 x DAL

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P42212
Unit cell:
a: 47.148Å b: 47.148Å c: 50.643Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.16 0.177
Expression system: Escherichia coli

Quick links

Citations

7 review citations

The roles of antimicrobial peptides in innate host defense.
Diamond et al. (2009)
6 more

1 mention without citation

Invariant gly residue is important for α-defensin folding, dimerization, and function: a case study of the human neutrophil α-defensin HNP1.
Zhao et al. (2012)