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: 29.41 kDa 
• Atom Count: 2349 
• Modelled Residue Count: 257 
• Deposited Residue Count: 258 
• Unique protein chains: 1

3S72

The origin of the hydrophobic effect in the molecular recognition of arylsulfonamides by carbonic anhydrase

• PDB DOI: 10.2210/pdb3S72/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-05-26 Released: 2011-10-19 
• Deposition Author(s): Snyder, P.W., Heroux, A., Whitesides, G.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.199 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

Literature

Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase.

Snyder, P.W., Mecinovic, J., Moustakas, D.T., Thomas, S.W., Harder, M., Mack, E.T., Lockett, M.R., Heroux, A., Sherman, W., Whitesides, G.M.

(2011) Proc Natl Acad Sci U S A 108: 17889-17894

• PubMed: 22011572 
• DOI: 10.1073/pnas.1114107108
• Primary Citation of Related Structures:  
  3S71, 3S72, 3S73, 3S74, 3S75, 3S76, 3S77, 3S78


• PubMed Abstract: 
  

The hydrophobic effect--a rationalization of the insolubility of nonpolar molecules in water--is centrally important to biomolecular recognition. Despite extensive research devoted to the hydrophobic effect, its molecular mechanisms remain controversial, and there are still no reliably predictive models for its role in protein-ligand binding. Here we describe a particularly well-defined system of protein and ligands--carbonic anhydrase and a series of structurally homologous heterocyclic aromatic sulfonamides--that we use to characterize hydrophobic interactions thermodynamically and structurally. In binding to this structurally rigid protein, a set of ligands (also defined to be structurally rigid) shows the expected gain in binding free energy as hydrophobic surface area is added. Isothermal titration calorimetry demonstrates that enthalpy determines these increases in binding affinity, and that changes in the heat capacity of binding are negative. X-ray crystallography and molecular dynamics simulations are compatible with the proposal that the differences in binding between the homologous ligands stem from changes in the number and organization of water molecules localized in the active site in the bound complexes, rather than (or perhaps in addition to) release of structured water from the apposed hydrophobic surfaces. These results support the hypothesis that structured water molecules--including both the molecules of water displaced by the ligands and those reorganized upon ligand binding--determine the thermodynamics of binding of these ligands at the active site of the protein. Hydrophobic effects in various contexts have different structural and thermodynamic origins, although all may be manifestations of the differences in characteristics of bulk water and water close to hydrophobic surfaces.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A [auth B]	258	Homo sapiens	Mutation(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 GTEx:  ENSG00000104267

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EVE	C [auth B]	1H-benzimidazole-2-sulfonamide C7 H7 N3 O2 S XRGHQBXKSHAQRB-UHFFFAOYSA-N
DMS	D [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EVE	PDBBind:  3S72	Kd: 400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.199 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.13	α = 90
b = 41.449	β = 104.53
c = 72.524	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-26 
• Released Date: 2011-10-19 
Deposition Author(s): Snyder, P.W., Heroux, A., Whitesides, G.W.

Revision History  

• Version 1.0: 2011-10-19
  Type: Initial release
  
• Version 1.1: 2011-12-21
  Changes: Database references