6SHK | pdb_00006shk

High resolution structure of the antimicrobial peptide Dermcidin from human

• PDB DOI: https://doi.org/10.2210/pdb6SHK/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2019-08-07 Released: 2019-09-25 
• Deposition Author(s): Zeth, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.281 (Depositor), 0.283 (DCC) 
• R-Value Observed: 
  0.281 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure and Functional Mechanism of a Human Antimicrobial Membrane Channel

Zeth, K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 4.96 kDa 
• Atom Count: 339 
• Modeled Residue Count: 48 
• Deposited Residue Count: 48 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dermcidin	A	48	Homo sapiens	Mutation(s): 0  Gene Names: DCD, AIDD, DSEP EC: 3.4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P81605 (Homo sapiens) Explore P81605  Go to UniProtKB:  P81605
PHAROS:  P81605 GTEx:  ENSG00000161634

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.281 (Depositor), 0.283 (DCC) 
• R-Value Observed: 0.281 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.758	α = 90
b = 50.758	β = 90
c = 105.88	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Zeth, K.

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary