Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 29411.54 
• Atom Count: 2085 
• Residue Count: 258 
• Unique protein chains: 1

3S72

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

• DOI: 10.2210/pdb3S72/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• 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: 1.6 Å
• R-Value Free: 0.199 
• R-Value Work: 0.159 

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.USA 108: 17889-17894

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


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Carbonic anhydrase 2	B	258	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens) Go to Gene View: CA2 Go to UniProtKB:  P00918

Small Molecules

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
EVE	Kd: 400 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.199 
• R-Value Work: 0.159 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 42.130	α = 90.00
b = 41.449	β = 104.53
c = 72.524	γ = 90.00

Software Package:

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

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
  Type: Database references