Biological Assembly 1  

 3D View: Structure | 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: 30.50 kDa 
• Atom Count: 2585 
• Modelled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

4WW6

Crystal structure of human carbonic anhydrase isozyme II with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide

• DOI: 10.2210/pdb4WW6/pdb

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


• Deposited: 2014-11-10 Released: 2015-07-01 
• Deposition Author(s): Smirnov, A., Manakova, E., Grazulis, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.151 
• R-Value Work: 0.128 
• R-Value Observed: 0.131 

Literature

Intrinsic thermodynamics of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamide binding to carbonic anhydrases by isothermal titration calorimetry.

Zubriene, A., Smirnoviene, J., Smirnov, A., Morkunaite, V., Michailoviene, V., Jachno, J., Juozapaitiene, V., Norvaisas, P., Manakova, E., Grazulis, S., Matulis, D.

(2015) Biophys Chem 205: 51-65

• PubMed: 26079542 
• DOI: 10.1016/j.bpc.2015.05.009
• Primary Citation of Related Structures:  
  4WR7, 4WUP, 4WUQ, 4WW6, 4WW8


• PubMed Abstract: 
  

Para substituted tetrafluorobenzenesulfonamides bind to carbonic anhydrases (CAs) extremely tightly and exhibit some of the strongest known protein-small ligand interactions, reaching an intrinsic affinity of 2 pM as determined by displacement isothermal titration calorimetry (ITC). The enthalpy and entropy of binding to five CA isoforms were measured by ITC in two buffers of different protonation enthalpies. The pKa values of compound sulfonamide groups were measured potentiometrically and spectrophotometrically, and enthalpies of protonation were measured by ITC in order to evaluate the proton linkage contributions to the observed binding thermodynamics. Intrinsic means the affinity of a sulfonamide anion for the Zn bound water form of CAs. Fluorination of the benzene ring significantly enhanced the observed affinities as it increased the fraction of deprotonated ligand while having little impact on intrinsic affinities. Intrinsic enthalpy contributions to the binding affinity were dominant over entropy and were more exothermic for CA I than for other CA isoforms. Thermodynamic measurements together with the X-ray crystallographic structures of protein-ligand complexes enabled analysis of structure-activity relationships in this enzyme ligand system.

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Organizational Affiliation: 

Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania.

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
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
3TV (Subject of Investigation/LOI)	G [auth A], H [auth A]	2,3,5,6-tetrafluoro-4-(propylsulfanyl)benzenesulfonamide C9 H9 F4 N O2 S2 LKPIFWBRFVJTMY-UHFFFAOYSA-N
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
BCN (Subject of Investigation/LOI)	F [auth A]	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N
MLA	E [auth A]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3TV	BindingDB:  4WW6	Kd: min: 0.91, max: 2 (nM) from 2 assay(s)
	Binding MOAD:  4WW6	Kd: 0.06 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.151 
• R-Value Work: 0.128 
• R-Value Observed: 0.131 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.214	α = 90
b = 41.026	β = 104.29
c = 71.774	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PDB_EXTRACT	data extraction
SCALA	data scaling
Coot	model building
MOLREP	phasing
REFMAC	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2014-11-10 
• Released Date: 2015-07-01 
Deposition Author(s): Smirnov, A., Manakova, E., Grazulis, S.

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Data collection