2YMK

Crystal structure of the hexameric anti-microbial peptide channel dermcidin

Structural Biology Knowledgebase: 2YMK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YMK

Classification: ANTIBIOTIC

Total Structure Weight: 14871.93

Macromolecule Entities
Molecule Chains Length Organism Details
DCD-1 A, B, C 48 Homo sapiens EC#: 3.4 IUBMB
Fragment: PEPTIDE, RESIDUES 63-110
Details: PEPTIDE OF 48 RESIDUES
Gene Name(s): DCD Gene View AIDD DSEP

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Adventitious Membrane Proteins: Alpha-helical Pore-forming Toxins.

Protein Name: Dermicidin hexameric anti-microbial peptide channel


Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A, B, C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.205
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 76.35 α = 90.00
b = 50.72 β = 117.74
c = 45.74 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-09
  • Released Date: 2012-10-17
  • Deposition author(s): Zeth, K.

Revision History

  • 2013-12-25
    Type: Polymer description | Details: COMPND
  • 2013-12-25
    Type: Citation | Details: JRNL
  • 2013-04-03
    Type: Citation | Details: JRNL
  • 2013-03-06
    Type: Citation | Details: JRNL
  • 2013-03-06
    Type: Other | Details: REMARK 280