1ZMI Antimicrobial Protein date May 10, 2005
title Crystal Structure Of Human Alpha_defensin-2 (Variant Gly16-> 32 2 1 Space Group )
authors J.Lubkowski, A.Prahl, W.Lu
compound source
Molecule: Neutrophil Defensin 2
Chain: A, B, C, D
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 32 2 1
R_factor 0.168 R_Free 0.182
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.685 71.685 54.882 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.15 Å
ligand DAL, GOL, SO4 enzyme
note 1ZMI is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, 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] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (1zmi.pdb1.gz) 24 Kb
  • Biological Unit Coordinates (1zmi.pdb2.gz) 22 Kb
  • Biological Unit Coordinates (1zmi.pdb3.gz) 86 Kb
  • Biological Unit Coordinates (1zmi.pdb4.gz) 44 Kb
  • Biological Unit Coordinates (1zmi.pdb5.gz) 44 Kb
  • Biological Unit Coordinates (1zmi.pdb6.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 1ZMI
  • CSU: Contacts of Structural Units for 1ZMI
  • Likely Quarternary Molecular Structure file(s) for 1ZMI
  • Structure Factors (567 Kb)
  • Retrieve 1ZMI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1ZMI from S2C, [Save to disk]
  • Re-refined 1zmi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1ZMI 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 1ZMI
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1ZMI, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1zmi_B] [1zmi_C] [1zmi_D] [1zmi] [1zmi_A]
  • SWISS-PROT database: [P59666]
  • Domain organization of [DEF3_HUMAN] by SWISSPFAM
  • Domain found in 1ZMI: [DEFSN ] by SMART
  • Other resources with information on 1ZMI
  • Community annotation for 1ZMI 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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