3GNY Antimicrobial Protein date Mar 18, 2009
title Crystal Structure Of Human Alpha-Defensin 1 (Hnp1)
authors M.Pazgier, W.Y.Lu
compound source
Molecule: Neutrophil Defensin 1
Chain: A, B
Synonym: Hnp-1, Hp-1, Hp1, Defensin, Alpha 1, Hp 1-56, Neut Defensin 2, Hnp-2, Hp-2, Hp2;
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 2
R_factor 0.171 R_Free 0.195
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.466 31.339 40.205 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.56 Å
ligand CL, GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThrough the looking glass, mechanistic insights from enantiomeric human defensins., Wei G, de Leeuw E, Pazgier M, Yuan W, Zou G, Wang J, Ericksen B, Lu WY, Lehrer RI, Lu W, J Biol Chem. 2009 Oct 16;284(42):29180-92. Epub 2009 Jul 29. PMID:19640840
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (16 Kb) [Save to disk]
  • Biological Unit Coordinates (3gny.pdb1.gz) 22 Kb
  • Biological Unit Coordinates (3gny.pdb2.gz) 11 Kb
  • LPC: Ligand-Protein Contacts for 3GNY
  • CSU: Contacts of Structural Units for 3GNY
  • Likely Quarternary Molecular Structure file(s) for 3GNY
  • Structure Factors (90 Kb)
  • Retrieve 3GNY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GNY from S2C, [Save to disk]
  • Re-refined 3gny structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GNY 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 3GNY
  • 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 3GNY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gny_B] [3gny] [3gny_A]
  • SWISS-PROT database: [P59665]
  • Belongs to the defensin (defensin) family according to TCDB.
  • Domain organization of [DEF1_HUMAN] by SWISSPFAM
  • Domain found in 3GNY: [DEFSN ] by SMART
  • Other resources with information on 3GNY
  • Community annotation for 3GNY 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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