6Z2Z

M2 mutant (R111K:Y134F:T54V:R132Q:P39Y:R59Y) of human cellular retinoic acid binding protein II - 2a conjugate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.265 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q5WClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Xanthopsin-Like Systems via Site-Specific Click-Functionalization of a Retinoic Acid Binding Protein.

Tassone, G.Paolino, M.Pozzi, C.Reale, A.Salvini, L.Giorgi, G.Orlandini, M.Galvagni, F.Mangani, S.Yang, X.Carlotti, B.Ortica, F.Latterini, L.Olivucci, M.Cappelli, A.

(2022) Chembiochem 23: e202100449-e202100449

  • DOI: https://doi.org/10.1002/cbic.202100449
  • Primary Citation of Related Structures:  
    6Z2U, 6Z2Z, 6ZSW, 6ZSX

  • PubMed Abstract: 

    The use of light-responsive proteins to control both living or synthetic cells, is at the core of the expanding fields of optogenetics and synthetic biology. It is thus apparent that a richer reaction toolbox for the preparation of such systems is of fundamental importance. Here, we provide a proof-of-principle demonstration that Morita-Baylis-Hillman adducts can be employed to perform a facile site-specific, irreversible and diastereoselective click-functionalization of a lysine residue buried into a lipophilic binding pocket and yielding an unnatural chromophore with an extended π-system. In doing so we effectively open the path to the in vitro preparation of a library of synthetic proteins structurally reminiscent of xanthopsin eubacterial photoreceptors. We argue that such a library, made of variable unnatural chromophores inserted in an easy-to-mutate and crystallize retinoic acid transporter, significantly expand the scope of the recently introduced rhodopsin mimics as both optogenetic and "lab-on-a-molecule" tools.


  • Organizational Affiliation

    Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100, Siena, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular retinoic acid-binding protein 2141Homo sapiensMutation(s): 6 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q5W (Subject of Investigation/LOI)
Query on Q5W

Download Ideal Coordinates CCD File 
B [auth A]methyl (~{Z})-3-(6-ethynylnaphthalen-2-yl)-2-methyl-prop-2-enoate
C17 H14 O2
RTMGYPGQEZWRAY-XFXZXTDPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.794α = 90
b = 58.794β = 90
c = 101.152γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q5WClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Data collection, Database references
  • Version 1.2: 2022-01-19
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary