3CYU

Human Carbonic Anhydrase II complexed with Cryptophane biosensor and xenon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure of a 129Xe-cryptophane biosensor complexed with human carbonic anhydrase II.

Aaron, J.A.Chambers, J.M.Jude, K.M.Di Costanzo, L.Dmochowski, I.J.Christianson, D.W.

(2008) J Am Chem Soc 130: 6942-6943

  • DOI: 10.1021/ja802214x
  • Primary Citation of Related Structures:  
    3CYU

  • PubMed Abstract: 
  • Cryptophanes represent an exciting class of xenon-encapsulating molecules that can be exploited as probes for nuclear magnetic resonance imaging. The 1.70 A resolution crystal structure of a cryptophane-derivatized benezenesulfonamide complexed with human carbonic anhydrase II shows how an encapsulated xenon atom can be directed to a specific biological target ...

    Cryptophanes represent an exciting class of xenon-encapsulating molecules that can be exploited as probes for nuclear magnetic resonance imaging. The 1.70 A resolution crystal structure of a cryptophane-derivatized benezenesulfonamide complexed with human carbonic anhydrase II shows how an encapsulated xenon atom can be directed to a specific biological target. The crystal structure confirms binding measurements indicating that the cryptophane cage does not strongly interact with the surface of the protein, which may enhance the sensitivity of 129Xe NMR spectroscopic measurements in solution.


    Organizational Affiliation

    Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1CR (Subject of Investigation/LOI)
Query on 1CR

Download Ideal Coordinates CCD File 
D [auth A]PoPo-2-[4-(2-(4-(methoxy)-1H-1,2,3-triazol-1-yl)ethyl)benzenesulfonamide]-7,12-bis-[3-(4-(methoxy)-1H-1,2,3-triazol-1-yl)propanoic acid]-cryptophane-A
C74 H74 N10 O18 S
SAIYTGCUDKIERP-UHFFFAOYSA-N
 Ligand Interaction
0CR (Subject of Investigation/LOI)
Query on 0CR

Download Ideal Coordinates CCD File 
C [auth A]MoMo-2-[4-(2-(4-(methoxy)-1H-1,2,3-triazol-1-yl)ethyl)benzenesulfonamide]-7,12-bis-[3-(4-(methoxy)-1H-1,2,3-triazol-1-y l)propanoic acid]-cryptophane-A
C74 H74 N10 O18 S
SAIYTGCUDKIERP-UHFFFAOYSA-N
 Ligand Interaction
XE
Query on XE

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0CR Binding MOAD:  3CYU Kd: 60 (nM) from 1 assay(s)
OCR PDBBind:  3CYU Kd: 60 (nM) from 1 assay(s)
1CR Binding MOAD:  3CYU Kd: 60 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.441α = 90
b = 49.985β = 107.13
c = 81.038γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance