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 Biol 9: 131-136

  • DOI: 10.1038/nsb754
  • Primary Citation of Related Structures:  
    1J78, 1J7E

  • 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 we report the 2 ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
vitamin D binding proteinA, B458Homo sapiensMutation(s): 1 
Gene Names: GC
UniProt & NIH Common Fund Data Resources
Find proteins for P02774 (Homo sapiens)
Explore P02774 
Go to UniProtKB:  P02774
PHAROS:  P02774
GTEx:  ENSG00000145321
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VDY
Query on VDY
Download Ideal Coordinates CCD File 
 F [auth B]3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL
C27 H44 O2
JWUBBDSIWDLEOM-DTOXIADCSA-N		 Ligand Interaction
OLA
Query on OLA
Download Ideal Coordinates CCD File 
 C [auth A], D [auth B], E [auth B]OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-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
b = 132.248β = 90
c = 73.179γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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