› 2ymk

X-ray diffraction
2.49Å resolution

Crystal structure of the hexameric anti-microbial peptide channel dermcidin

Released:
DOI: 10.2210/pdb2ymk/pdb
PDB entry 2ymk coloured by chain, front view.
PDB entry 2ymk coloured by chain, side view.
PDB entry 2ymk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure and functional mechanism of a human antimicrobial membrane channel.
Song C, Weichbrodt C, Salnikov ES, Dynowski M, Forsberg BO, Bechinger B, Steinem C, de Groot BL, Zachariae U, Zeth K
Proc Natl Acad Sci U S A 110 4586-91 (2013)
PMID: 23426625

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-160539 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DCD-1 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 48 amino acids
Theoretical weight: 4.83 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P81605 (Residues: 63-110; Coverage: 53%)
Gene names: AIDD, DCD, DSEP
Sequence domains: Dermcidin, antibiotic peptide
Structure domains: Single helix bin

Ligands and Environments

1 bound ligand:
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: C2
Unit cell:
a: 76.354Å b: 50.724Å c: 45.738Å
α: 90° β: 117.74° γ: 90°
R-values:
R R work R free
0.208 0.205 0.274
Expression system: Not provided

Quick links

Citations

21 review citations

Antimicrobial peptides in 2014.
Wang et al. (2015)
20 more

5 mentions without citation

The role of bacterial transport systems in the removal of host antimicrobial peptides in Gram-negative bacteria.
Blair et al. (2022)
4 more