3CYU

Human Carbonic Anhydrase II complexed with Cryptophane biosensor and xenon

• PDB DOI: https://doi.org/10.2210/pdb3CYU/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-26 Released: 2008-05-27 
• Deposition Author(s): Aaron, J.A., Jude, K.M., Di Costanzo, L., Christianson, D.W.

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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 

Starting Model: experimental

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

• PubMed: 18461940 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.46 kDa 
• Atom Count: 2,443 
• Modelled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1CR	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
0CR	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
XE	E [auth A], F [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OCR	PDBBind:  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 = 67.441	α = 90
b = 49.985	β = 107.13
c = 81.038	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Aaron, J.A., Jude, K.M., Di Costanzo, L., Christianson, D.W.

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary