Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 103.80 kDa 
• Atom Count: 7137 
• Residue Count: 880 
• Unique protein chains: 1

1J78

Crystallographic analysis of the human vitamin D binding protein

• DOI: 10.2210/pdb1J78/pdb

• Classification: TRANSPORT, LIGAND BINDING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2001-05-16 Released: 2002-02-06 
• Deposition Author(s): Verboven, C., Rabijns, A., De Maeyer, M., Van Baelen, H., Bouillon, R., De Ranter, C.

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Experimental Data Snapshot

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

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

• PubMed: 11799400 
• DOI: 10.1038/nsb754
• Structures With Same Primary Citation


• 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 2.3 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
vitamin D binding protein	A, B	458	Homo sapiens	Mutation(s): 1  Gene Names: GC
Find proteins for P02774 (Homo sapiens) Go to UniProtKB:  P02774
NIH Common Fund Data Resources
PHAROS  P02774 GTEx  ENSG00000145321

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VDY	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
OLA	A, B	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N

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 = 132.248	α = 90
b = 132.248	β = 90
c = 73.179	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-05-16 
• Released Date: 2002-02-06 
Deposition Author(s): Verboven, C., Rabijns, A., De Maeyer, M., Van Baelen, H., Bouillon, R., De Ranter, C.

Revision History 

• 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