2PM4 Antimicrobial Protein date Apr 20, 2007
title Human Alpha-Defensin 1 (Multiple Arg->Lys Mutant)
authors J.Lubkowski, M.Pazgier, W.Lu
compound source
Molecule: Neutrophil Defensin 1 (Hnp-1) (Hp-1) (Hp1) (Defen 1);
Chain: A, B
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Defa1, Def1, Defa2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 42 2 2
R_factor 0.192 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.383 41.383 97.165 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceToward understanding the cationicity of defensins. Arg and Lys versus their noncoded analogs., Zou G, de Leeuw E, Li C, Pazgier M, Li C, Zeng P, Lu WY, Lubkowski J, Lu W, J Biol Chem. 2007 Jul 6;282(27):19653-65. Epub 2007 Apr 23. PMID:17452329
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (16 Kb) [Save to disk]
  • Biological Unit Coordinates (2pm4.pdb1.gz) 10 Kb
  • Biological Unit Coordinates (2pm4.pdb2.gz) 8 Kb
  • CSU: Contacts of Structural Units for 2PM4
  • Likely Quarternary Molecular Structure file(s) for 2PM4
  • Structure Factors (57 Kb)
  • Retrieve 2PM4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PM4 from S2C, [Save to disk]
  • Re-refined 2pm4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2PM4 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 2PM4
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2PM4, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pm4_B] [2pm4] [2pm4_A]
  • SWISS-PROT database: [P59666]
  • Domain organization of [DEF3_HUMAN] by SWISSPFAM
  • Domain found in 2PM4: [DEFSN ] by SMART
  • Other resources with information on 2PM4
  • Community annotation for 2PM4 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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