1J78

Crystallographic analysis of the human vitamin D binding protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

A structural basis for the unique binding features of the human vitamin D-binding protein.

Verboven, C., Rabijns, A., De Maeyer, M., Van Baelen, H., Bouillon, R., De Ranter, C.

(2002) Nat.Struct.Mol.Biol. 9: 131-136

  • DOI: 10.1038/nsb754
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The human serum vitamin D-binding protein (DBP) has many physiologically important functions, ranging from transporting vitamin D3 metabolites, binding and sequestering globular actin and binding fatty acids to functioning in the immune system. Here ...

    The human serum vitamin D-binding protein (DBP) has many physiologically important functions, ranging from transporting vitamin D3 metabolites, binding and sequestering globular actin and binding fatty acids to functioning in the immune system. Here we report the 2.3 A crystal structure of DBP in complex with 25-hydroxyvitamin D3, a vitamin D3 metabolite, which reveals the vitamin D-binding site in the N-terminal part of domain I. To more explicitly explore this, we also studied the structure of DBP in complex with a vitamin D3 analog. Comparisons with the structure of human serum albumin, another family member, reveal a similar topology but also significant differences in overall, as well as local, folding. These observed structural differences explain the unique vitamin D3-binding property of DBP.

    Organizational Affiliation: 

    Laboratorium voor Analytische Chemie en Medicinale Fysicochemie, Faculteit Farmaceutische Wetenschappen, Katholieke Universiteit Leuven, E. Van Evenstraat 4, B-3000 Leuven, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
vitamin D binding protein
A, B
458Homo sapiensMutation(s): 0 
Gene Names: GC
Find proteins for P02774 (Homo sapiens)
Go to Gene View: GC
Go to UniProtKB:  P02774
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLA
Query on OLA
Download SDF File 
Download CCD File 
A, B
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
VDY
Query on VDY
Download SDF File 
Download CCD File 
B
3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL
25-HYDROXYVITAMIN D3
C27 H44 O2
JWUBBDSIWDLEOM-DTOXIADCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.220 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 132.248α = 90.00
b = 132.248β = 90.00
c = 73.179γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SHARPphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation