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- PDB-5sz0: Carbonic anhydrase II in complex with 4-(phenyl)-benzenesulfonamide -

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Basic information

Entry
Database: PDB / ID: 5sz0
TitleCarbonic anhydrase II in complex with 4-(phenyl)-benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / sulfonamide / inhibitor / zinc-binding / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase ...Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
4-(phenyl)-benzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsBhatt, A. / Mahon, B.P. / Cornelio, B. / McKenna, R.
CitationJournal: Chembiochem / Year: 2017
Title: Structure-Activity Relationships of Benzenesulfonamide-Based Inhibitors towards Carbonic Anhydrase Isoform Specificity.
Authors: Bhatt, A. / Mahon, B.P. / Cruzeiro, V.W. / Cornelio, B. / Laronze-Cochard, M. / Ceruso, M. / Sapi, J. / Rance, G.A. / Khlobystov, A.N. / Fontana, A. / Roitberg, A. / Supuran, C.T. / McKenna, R.
History
DepositionAug 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3094
Polymers28,9331
Non-polymers3773
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.406, 41.377, 72.042
Angle α, β, γ (deg.)90.000, 104.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 28932.641 Da / Num. of mol.: 1 / Fragment: UNP residues 4-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-72D / 4-(phenyl)-benzenesulfonamide / [1,1'-biphenyl]-4-sulfonamide


Mass: 233.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11NO2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 1.6M Sodium Citrate, 50mM Tris pH 7.8 / PH range: 7.2-8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.63→20 Å / Num. obs: 48127 / % possible obs: 95.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.069 / Net I/av σ(I): 18.683 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.63-1.662.90.4340.842179.1
1.66-1.693.50.4590.845190
1.69-1.724.10.4010.884194
1.72-1.764.60.3870.9193.8
1.76-1.794.70.3460.922195.5
1.79-1.844.90.2940.941194.4
1.84-1.884.90.2340.961196.6
1.88-1.9350.2010.963195.2
1.93-1.9950.1620.98197.4
1.99-2.0550.140.98196.3
2.05-2.135.10.1150.988196.3
2.13-2.215.10.0970.989198.2
2.21-2.315.10.0860.989198
2.31-2.4350.0790.988198
2.43-2.595.10.0740.992198.1
2.59-2.795.10.0620.993198.6
2.79-3.065.10.0530.995199
3.06-3.515.10.0430.997199.4
3.51-4.415.10.0390.997199.5
4.41-204.80.0520.982199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10pre_2097refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.63→19.978 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.89
RfactorNum. reflection% reflection
Rfree0.1924 2405 5 %
Rwork0.1651 --
obs0.1664 48127 81.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.01 Å2 / Biso mean: 18.6622 Å2 / Biso min: 8.14 Å2
Refinement stepCycle: final / Resolution: 1.63→19.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 33 161 2243
Biso mean--30.37 25.03 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062148
X-RAY DIFFRACTIONf_angle_d0.8882916
X-RAY DIFFRACTIONf_chiral_restr0.054301
X-RAY DIFFRACTIONf_plane_restr0.005377
X-RAY DIFFRACTIONf_dihedral_angle_d10.0941258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6289-1.66210.3009670.29811289135639
1.6621-1.69820.2666990.24651692179151
1.6982-1.73770.25031000.20131901200158
1.7377-1.78120.22981070.18812030213762
1.7812-1.82930.17871210.18182266238768
1.8293-1.88310.20731220.18982509263175
1.8831-1.94380.18671400.17432674281480
1.9438-2.01320.18311590.16442801296085
2.0132-2.09370.20031560.15792997315391
2.0937-2.18890.21711710.15633146331794
2.1889-2.30420.2131600.15443175333596
2.3042-2.44830.18851730.17063161333496
2.4483-2.63690.20751550.1733200335596
2.6369-2.90160.19421730.18463207338097
2.9016-3.31980.21211700.17543240341097
3.3198-4.17630.15441680.14183218338697
4.1763-19.97970.16591660.14033214338097
Refinement TLS params.Method: refined / Origin x: -6.0973 Å / Origin y: -2.6606 Å / Origin z: 85.6973 Å
111213212223313233
T0.0267 Å20.0005 Å2-0.0001 Å2-0.0224 Å2-0.0005 Å2--0.0276 Å2
L0.2906 °2-0.0614 °2-0.0153 °2-0.1089 °2-0.0368 °2--0.2317 °2
S-0.0051 Å °-0.0213 Å °0.0061 Å °-0.012 Å °0.0036 Å °0.0097 Å °0.0065 Å °0.0061 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 104
4X-RAY DIFFRACTION1allD105 - 163
5X-RAY DIFFRACTION1allC2
6X-RAY DIFFRACTION1allE1

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