2NDK Hydrolase date Jun 29, 2016
title 20 Lowest Energy Ensemble Of Dermcidin (Dcd1l) Nmr Structure
authors K.W.Tan, Y.K.Mok
compound source
Molecule: Dermcidin
Chain: A
Fragment: Unp Residues 63-110
Synonym: Preproteolysin, Survival-Promoting Peptide, Dcd-1
Ec: 3.4.-.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dcd, Aidd, Dsep
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector: N.A.
methodSolution NMR
enzyme Hydrolase E.C.3.4 BRENDA
subcellular loc. Membrane localization by OPM: Secreted
out side
in side
Primary referenceStructural basis for the bacterial membrane insertion of dermcidin peptide, DCD-1L., Nguyen VS, Tan KW, Ramesh K, Chew FT, Mok YK, Sci Rep. 2017 Oct 24;7(1):13923. doi: 10.1038/s41598-017-13600-z. PMID:29066724
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (233 Kb) [Save to disk]
  • Biological Unit Coordinates (2ndk.pdb1.gz) 12 Kb
  • CSU: Contacts of Structural Units for 2NDK
  • Original NMR restraints for 2NDK from PDB
  • Retrieve 2NDK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NDK from S2C, [Save to disk]
  • View 2NDK 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 2NDK
  • 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
  • Fold representative 2ndk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ndk_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2NDK
  • Community annotation for 2NDK at PDBWiki (http://pdbwiki.org)

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