Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 30.20 kDa 
• Atom Count: 2522 
• Modelled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

4FIK

Human carbonic anhydrase II H64A complexed with thioxolone hydrolysis products

• PDB DOI: 10.2210/pdb4FIK/pdb
• Entry: 4FIK supersedes: 3IQK

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-06-08 Released: 2012-06-27 
• Deposition Author(s): Sippel, K.H., Genis, C., Govindasamy, L., Agbandje-McKenna, M., Tripp, B.C., McKenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.137 
• R-Value Work: 0.116 
• R-Value Observed: 0.117 

Literature

Synchrotron Radiation Provides a Plausible Explanation for the Generation of a Free Radical Adduct of Thioxolone in Mutant Carbonic Anhydrase II.

Sippel, K.H., Genis, C., Govindasamy, L., Agbandje-McKenna, M., Kiddle, J.J., Tripp, B.C., McKenna, R.

(2010) J Phys Chem Lett 1: 2898-2902

• PubMed: 20976122 
• DOI: 10.1021/jz100954h
• Primary Citation of Related Structures:  
  4FIK


• PubMed Abstract: 
  

Thioxolone acts as a prodrug in the presence of carbonic anhydrase II (CA II), whereby the molecule is cleaved by thioester hydrolysis to the carbonic anhydrase inhibitor, 4-mercaptobenzene-1,3-diol (TH0). Thioxolone was soaked into the proton transfer mutant H64A of CA II in an effort to capture a reaction intermediate via X-ray crystallography. Structure determination of the 1.2 Å resolution data revealed the TH0 had been modified to a 4,4'-disulfanediyldibenzene-1,3-diol, a product of crystallization conditions, and a zinc ligated 2,4-dihydroxybenzenesulfenic acid, most likely induced by radiation damage. Neither ligand was likely a result of an enzymatic mechanism.

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Related Citations: 

• Inhibition of Carbonic Anhydrase II by Thioxolone: A Mechanistic and Structural Study
  Barrese, A.A., Genis, C., Fisher, S.Z., Orwenyo, J.N., Kumara, M.T., Dutta, S.K., Phillips, E., Kiddle, J.J., Tu, C., Silverman, D.N., Govindasamy, L., Agbandje-McKenna, M., McKenna, R., Tripp, B.C.
  (2008) Biochemistry 47: 3174

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, P.O. Box 100245, College of Medicine, University of Florida, Gainesville, Florida 32610.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 1  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 GTEx:  ENSG00000104267

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D2S	E [auth A]	4,4'-disulfanediyldibenzene-1,3-diol C12 H10 O4 S2 DCHQLQXIXWXHFP-UHFFFAOYSA-N
TH7	C [auth A]	2,4-dihydroxybenzenesulfenic acid C6 H6 O3 S LJXFZIAMAZBGDO-UHFFFAOYSA-N
TH0	D [auth A], F [auth A]	4-MERCAPTOBENZENE-1,3-DIOL C6 H6 O2 S XFTQIEMOLHJTFV-UHFFFAOYSA-N
SO4	H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SO4	BindingDB:  4FIK	Ki: min: 8.90e+7, max: 3.00e+8 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.137 
• R-Value Work: 0.116 
• R-Value Observed: 0.117 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.37	α = 90
b = 41.38	β = 104.1
c = 72.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-08 
• Released Date: 2012-06-27 
Deposition Author(s): Sippel, K.H., Genis, C., Govindasamy, L., Agbandje-McKenna, M., Tripp, B.C., McKenna, R.
• This entry supersedes: 3IQK

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description