1ZMK Antimicrobial Protein date May 10, 2005
title Crystal Structure Of Human Alpha-Defensin-2 (Variant Gly16-> 42 21 2 Space Group
authors J.Lubkowski, A.Prahl, W.Lu
compound source
Molecule: Neutrophil Defensin 2
Chain: A, B
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Defa3, Def3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 42 21 2
R_factor 0.160 R_Free 0.177
length a length b length c angle alpha angle beta angle gamma
47.148 47.148 50.643 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.30 Å
ligand CL, DAL, GOL enzyme
A, B

Primary referenceReconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids., Xie C, Prahl A, Ericksen B, Wu Z, Zeng P, Li X, Lu WY, Lubkowski J, Lu W, J Biol Chem 2005 Sep 23;280(38):32921-9. Epub 2005 May 13. PMID:15894545
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (1zmk.pdb1.gz) 24 Kb
  • Biological Unit Coordinates (1zmk.pdb2.gz) 90 Kb
  • LPC: Ligand-Protein Contacts for 1ZMK
  • CSU: Contacts of Structural Units for 1ZMK
  • Likely Quarternary Molecular Structure file(s) for 1ZMK
  • Structure Factors (229 Kb)
  • Retrieve 1ZMK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1ZMK from S2C, [Save to disk]
  • Re-refined 1zmk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1ZMK 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 1ZMK
  • 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 1ZMK, from MSDmotif at EBI
  • Fold representative 1zmk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1zmk] [1zmk_B] [1zmk_A]
  • SWISS-PROT database: [P59666]
  • Domain organization of [DEF3_HUMAN] by SWISSPFAM
  • Domain found in 1ZMK: [DEFSN ] by SMART
  • Other resources with information on 1ZMK
  • Community annotation for 1ZMK at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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