2CBS

CELLULAR RETINOIC ACID BINDING PROTEIN II IN COMPLEX WITH A SYNTHETIC RETINOIC ACID (RO-13 6307)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.200 

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This is version 1.3 of the entry. See complete history


Literature

Structures of cellular retinoic acid binding proteins I and II in complex with synthetic retinoids.

Chaudhuri, B.N.Kleywegt, G.J.Broutin-L'Hermite, I.Bergfors, T.Senn, H.Le Motte, P.Partouche, O.Jones, T.A.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1850-1857

  • DOI: 10.1107/s0907444999011026
  • Primary Citation of Related Structures:  
    2CBR, 2CBS, 3CBS

  • PubMed Abstract: 
  • Retinoids play important roles in diverse cellular processes including growth, cell differentiation and vision. Many natural and synthetic retinoids are used as drugs in dermatology and oncology. A large amount of data has been accumulated on the cellular activity of different synthetic retinoids ...

    Retinoids play important roles in diverse cellular processes including growth, cell differentiation and vision. Many natural and synthetic retinoids are used as drugs in dermatology and oncology. A large amount of data has been accumulated on the cellular activity of different synthetic retinoids. They are stabilized and transported inside the cell cytoplasm by binding and transport proteins, such as cellular retinol-binding proteins and cellular retinoic acid binding proteins (CRABPs). The structures of human CRABP II in complex with two different synthetic retinoids, Ro13-6307 and Ro12--7310 (at 2.1 and 2.0 A resolution, respectively) and of bovine CRABP I in complex with a retinobenzoic acid, Am80 (at 2.8 A resolution) are described. The binding affinities of human CRABP I and II for the retinoids studied here have been determined. All these compounds have comparable binding affinities (nanomolar range) for both CRABPs. Apart from the particular interactions of the carboxylate group of the retinoids with specific protein groups, each structure reveals characteristic interactions. Studying the atomic details of the interaction of retinoids with retinoid-binding proteins facilitates the understanding of the kinetics of retinoid trafficking inside the cytoplasm.


    Related Citations: 
    • Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid.
      Kleywegt, G.J., Bergfors, T., Senn, H., Le Motte, P., Gsell, B., Shudo, K., Jones, T.A.
      (1994) Structure 2: 1241
    • Lipid-binding proteins: a family of fatty acid and retinoid transport proteins.
      Banaszak, L., Winter, N., Xu, Z., Bernlohr, D.A., Cowan, S., Jones, T.A.
      (1994) Adv Protein Chem 45: 89
    • Crystallization and preliminary X-ray analysis of recombinant bovine cellular retinoic acid-binding protein.
      Bergfors, T., Kleywegt, G.J., Jones, T.A.
      (1994) Acta Crystallogr D Biol Crystallogr 50: 370

    Organizational Affiliation

    Department of Cell Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24, Uppsala, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CRABP-II)A137Homo sapiensMutation(s): 0 
Gene Names: CRABP2
UniProt & NIH Common Fund Data Resources
Find proteins for P29373 (Homo sapiens)
Explore P29373 
Go to UniProtKB:  P29373
PHAROS:  P29373
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29373
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R13
Query on R13

Download Ideal Coordinates CCD File 
B [auth A]3-METHYL-7-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRO-NAPHTHALEN-2-YL) -OCTA-2,4,6-TRIENOIC ACID
C23 H30 O2
HGGVUZHIUHCATB-OOUGZNGESA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
R13 Binding MOAD:  2CBS IC50: 6 (nM) from 1 assay(s)
PDBBind:  2CBS IC50: 6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.25α = 90
b = 47.64β = 90
c = 74.83γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-22
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-06
    Changes: Data collection, Database references