1IJV | pdb_00001ijv

HUMAN BETA-DEFENSIN-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.193 (Depositor), 0.189 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1IJV

This is version 1.3 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 Biological Chem 276: 39021-39026

  • DOI: https://doi.org/10.1074/jbc.M103830200
  • Primary Citation Related Structures: 
    1IJU, 1IJV

  • 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, 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.

Macromolecule Content 

  • Total Structure Weight: 8.59 kDa 
  • Atom Count: 796 
  • Modeled Residue Count: 72 
  • Deposited Residue Count: 72 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-defensin 1
A, B
36N/AMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P60022 (Homo sapiens)
Explore P60022 
Go to UniProtKB:  P60022
PHAROS:  P60022
GTEx:  ENSG00000164825 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60022
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
BR

Query on BR



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
K

Query on K



Download:Ideal Coordinates CCD File
K [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.193 (Depositor), 0.189 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.121α = 90
b = 47.243β = 90
c = 53.853γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHARPphasing
DMmodel building
SHELXL-97refinement
SHELXphasing
DMphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Version format compliance
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary