1FEN | pdb_00001fen

CRYSTALLOGRAPHIC STUDIES ON COMPLEXES BETWEEN RETINOIDS AND PLASMA RETINOL-BINDING PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1FEN

This is version 1.3 of the entry. See complete history

Literature

Crystallographic studies on complexes between retinoids and plasma retinol-binding protein.

Zanotti, G.Marcello, M.Malpeli, G.Folli, C.Sartori, G.Berni, R.

(1994) J Biological Chem 269: 29613-29620

  • Primary Citation Related Structures: 
    1FEL, 1FEM, 1FEN

  • PubMed Abstract: 

    The three-dimensional structures of complexes between bovine plasma retinol-binding protein (RBP) and three retinol analogs with different end groups (fenretinide, all-trans retinoic acid, and axerophthene) have been determined to 1.8-1.9-A resolution. Their models are very similar to that of the bovine retinol.RBP complex: the root mean square deviations between equivalent alpha-carbons in the two proteins range from 0.17 to 0.24 A. The retinoid molecules fit in the beta-barrel cavity assuming the same conformation of the vitamin, and the substitutions have no consequences on the overall protein structure. While confirming that an intact hydroxyl end group is not an absolute requirement for a correct retinoid binding to RBP, this study has shown the occurrence of conformational changes, although limited, in the rather flexible loop region at the entrance of the beta-barrel upon fenretinide and retinoic acid binding. These changes are suitable for accommodating the end groups of the above retinoids. Instead, no such changes have been revealed in RBP complexed with axerophthene, a retinol analog bearing a hydrogen atom in place of the hydroxyl end group. The protein conformational changes in the above loop region, the steric hindrance of bulky end groups of bound retinoids, and the lack of the retinol hydroxyl group appear to be responsible for the possible reduced affinity of retinoids for RBP relative to retinol and, at the same time, for the abolished or reduced affinity of retinoid.RBP complexes for transthyretin relative to retinol-RBP.


  • Organizational Affiliation
    • Department of Organic Chemistry, University of Padova, Italy.

Macromolecule Content 

  • Total Structure Weight: 21.37 kDa 
  • Atom Count: 1,605 
  • Modeled Residue Count: 177 
  • Deposited Residue Count: 183 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RETINOL BINDING PROTEIN183Bos taurusMutation(s): 0 
UniProt
Find proteins for P18902 (Bos taurus)
Explore P18902 
Go to UniProtKB:  P18902
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18902
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AZE

Query on AZE



Download:Ideal Coordinates CCD File
B [auth A]ALL-TRANS AXEROPHTHENE
C20 H30
IDMGVRDNZFQORW-JWBAUCAFSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.38α = 90
b = 49.2β = 90
c = 76.65γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-11-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other