Crystal Structure of the R132K:Y134F:R111L:T54V:L121E Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-trans-Retinoic Acid at 1.57 Angstroms Resolution

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.125 

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Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding.

Vaezeslami, S.Jia, X.Vasileiou, C.Borhan, B.Geiger, J.H.

(2008) Acta Crystallogr D Biol Crystallogr 64: 1228-1239

  • DOI: https://doi.org/10.1107/S0907444908032216
  • Primary Citation of Related Structures:  
    3CWK, 3D95, 3D96

  • PubMed Abstract: 

    The structural integrity of cellular retinoic acid-binding protein II (CRABPII) has been investigated using the crystal structures of CRABPII mutants. The overall fold was well maintained by these CRABPII mutants, each of which carried multiple different mutations. A water-mediated network is found to be present across the large binding cavity, extending from Arg111 deep inside the cavity to the alpha2 helix at its entrance. This chain of interactions acts as a ;pillar' that maintains the integrity of the protein. The disruption of the water network upon loss of Arg111 leads to decreased structural integrity of the protein. A water-mediated network can be re-established by introducing the hydrophilic Glu121 inside the cavity, which results in a rigid protein with the alpha2 helix adopting an altered conformation compared with wild-type CRABPII.

  • Organizational Affiliation

    Rigaku Americas Corporation, 9009 New Trails Drive, The Woodlands, TX 77381, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular retinoic acid-binding protein 2137Homo sapiensMutation(s): 5 
Gene Names: CRABP2
UniProt & NIH Common Fund Data Resources
Find proteins for P29373 (Homo sapiens)
Explore P29373 
Go to UniProtKB:  P29373
PHAROS:  P29373
GTEx:  ENSG00000143320 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29373
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
REA Binding MOAD:  3CWK Kd: 250 (nM) from 1 assay(s)
PDBBind:  3CWK Kd: 250 (nM) from 1 assay(s)
BindingDB:  3CWK Kd: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.787α = 90
b = 44.86β = 90
c = 77.865γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-21
    Changes: Data collection