2YMK Antibiotic date Oct 09, 2012
title Crystal Structure Of The Hexameric Anti-Microbial Peptide Channel Dermcidin
authors K.Zeth
compound source
Molecule: Dcd-1
Chain: A, B, C
Fragment: Peptide, Residues 63-110
Synonym: Dermcidin, Preproteolysin, Survival-Promoting Pept
Ec: 3.4.-.-
Other_details: Peptide Of 48 Residues
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.20466 R_Free 0.27384
length a length b length c angle alpha angle beta angle gamma
76.354 50.724 45.738 90.00 117.74 90.00
method X-Ray Diffractionresolution 2.49 Å
ligand ZN enzyme Hydrolase E.C.3.4 BRENDA
note 2YMK (Molecule of the Month:pdb162)
subcellular loc. Membrane localization by OPM: Secreted
out side
in side
Primary referenceCrystal structure and functional mechanism of a human antimicrobial membrane channel., Song C, Weichbrodt C, S Salnikov E, Dynowski M, O Forsberg B, Bechinger B, Steinem C, de Groot BL, Zachariae U, Zeth K, Proc Natl Acad Sci U S A. 2013 Feb 20. PMID:23426625
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (2ymk.pdb1.gz) 82 Kb
  • LPC: Ligand-Protein Contacts for 2YMK
  • CSU: Contacts of Structural Units for 2YMK
  • Structure Factors (84 Kb)
  • Retrieve 2YMK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YMK from S2C, [Save to disk]
  • Re-refined 2ymk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YMK in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2YMK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2YMK, from MSDmotif at EBI
  • Fold representative 2ymk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ymk_A] [2ymk_B] [2ymk] [2ymk_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2YMK
  • Community annotation for 2YMK at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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