1IJV

HUMAN BETA-DEFENSIN-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of human beta-defensin-1: new insights into structural properties of beta-defensins.

Hoover, D.M.Chertov, O.Lubkowski, J.

(2001) J.Biol.Chem. 276: 39021-39026

  • DOI: 10.1074/jbc.M103830200
  • Primary Citation of Related Structures:  1IJU

  • PubMed Abstract: 
  • Defensins are a class of small cationic peptides found in higher organisms that serve as both antimicrobial and cell signaling molecules. The exact mechanism of the antimicrobial activity of defensins is not known, but two models have been postulated ...

    Defensins are a class of small cationic peptides found in higher organisms that serve as both antimicrobial and cell signaling molecules. The exact mechanism of the antimicrobial activity of defensins is not known, but two models have been postulated, one involving pore formation and the other involving nonspecific electrostatic interaction with the bacterial membrane. Here we report the high resolution structures of human beta-defensin-1 (hBD1) in two crystallographic space groups. The structure of a single molecule is very similar to that of human beta-defensin-2 (hBD2), confirming the presence of an N-terminal alpha-helix. However, while the packing of hBD1 is conserved across both space groups, there is no evidence for any larger quaternary structure similar to octameric hBD2. Furthermore, the topology of hBD1 dimers that are formed between monomers in the asymmetric unit is distinct from both hBD2 and other mammalian alpha-defensins. The structures of hBD1 and hBD2 provide a first step toward understanding the structural basis of antimicrobial and chemotactic properties of human beta-defensins.


    Organizational Affiliation

    Macromolecular Crystallography Laboratory and the Intramural Research Support Program, LMI, SAIC Frederick, NCI at Frederick, National Institutes of Health, Frederick, Maryland 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-defensin 1
A, B
36Homo sapiensGene Names: DEFB1 (BD1, HBD1)
Find proteins for P60022 (Homo sapiens)
Go to Gene View: DEFB1
Go to UniProtKB:  P60022
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BR
Query on BR

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Download CCD File 
A, B
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 27.121α = 90.00
b = 47.243β = 90.00
c = 53.853γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
SHELXmodel building
SHELXphasing
DMmodel building
SHARPphasing
DENZOdata reduction
DMphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Version format compliance