5EKJ | pdb_00005ekj

Human Carbonic Anhydrase II complexed with a two-faced guest


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 
    0.150 (Depositor), 0.150 (DCC) 
  • R-Value Work: 
    0.134 (Depositor), 0.130 (DCC) 
  • R-Value Observed: 
    0.135 (Depositor) 

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 TG4Click on this verticalbar to view details

This is version 1.6 of the entry. See complete history


Literature

Programming A Molecular Relay for Ultrasensitive Biodetection through (129) Xe NMR.

Wang, Y.Roose, B.W.Philbin, J.P.Doman, J.L.Dmochowski, I.J.

(2016) Angew Chem Int Ed Engl 55: 1733-1736

  • DOI: https://doi.org/10.1002/anie.201508990
  • Primary Citation of Related Structures:  
    5EKH, 5EKJ, 5EKM

  • PubMed Abstract: 

    A supramolecular strategy for detecting specific proteins in complex media by using hyperpolarized (129) Xe NMR is reported. A cucurbit[6]uril (CB[6])-based molecular relay was programmed for three sequential equilibrium conditions by designing a two-faced guest (TFG) that initially binds CB[6] and blocks the CB[6]-Xe interaction. The protein analyte recruits the TFG and frees CB[6] for Xe binding. TFGs containing CB[6]- and carbonic anhydrase II (CAII)-binding domains were synthesized in one or two steps. X-ray crystallography confirmed TFG binding to Zn(2+) in the deep CAII active-site cleft, which precludes simultaneous CB[6] binding. The molecular relay was reprogrammed to detect avidin by using a different TFG. Finally, Xe binding by CB[6] was detected in buffer and in E. coli cultures expressing CAII through ultrasensitive (129) Xe NMR spectroscopy.


  • Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA, 19104-6323, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 1 
Gene Names: CA2
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
GTEx:  ENSG00000104267 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free:  0.150 (Depositor), 0.150 (DCC) 
  • R-Value Work:  0.134 (Depositor), 0.130 (DCC) 
  • R-Value Observed: 0.135 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.35α = 90
b = 41.35β = 104.15
c = 72.13γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

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 TG4Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM097478

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-06
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references
  • Version 1.2: 2016-02-03
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-11-22
    Changes: Refinement description
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.6: 2024-03-06
    Changes: Data collection, Database references, Derived calculations