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- PDB-6b59: Carbonic anhydrase II in complex with nitrogenous base-bearing be... -

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Basic information

Entry
Database: PDB / ID: 6b59
TitleCarbonic anhydrase II in complex with nitrogenous base-bearing benezenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/INHIBITOR / carbonic anhydrase / inhibitor / benzenesulfonamide / purine / adenine / 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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / 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 / one-carbon metabolic process / 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
Chem-CQS / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.638 Å
AuthorsLomelino, C.L. / McKenna, R.M.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Discovery of New Sulfonamide Carbonic Anhydrase IX Inhibitors Incorporating Nitrogenous Bases.
Authors: Nocentini, A. / Bua, S. / Lomelino, C.L. / McKenna, R. / Menicatti, M. / Bartolucci, G. / Tenci, B. / Di Cesare Mannelli, L. / Ghelardini, C. / Gratteri, P. / Supuran, C.T.
History
DepositionSep 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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)29,5445
Polymers28,9331
Non-polymers6114
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-2 kcal/mol
Surface area11520 Å2
Unit cell
Length a, b, c (Å)42.646, 41.667, 72.633
Angle α, β, γ (deg.)90.000, 104.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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
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

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Non-polymers , 5 types, 159 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CQS / 2-(6-amino-9H-purin-9-yl)-N-[2-(4-sulfamoylphenyl)ethyl]acetamide


Mass: 375.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N7O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M NaCitrate 50mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.638→40.216 Å / Num. obs: 37853 / % possible obs: 86.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.12 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.029 / Rrim(I) all: 0.06 / Χ2: 0.863 / Net I/σ(I): 20.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.683.40.57213500.7160.340.670.83592
1.68-1.713.40.48313900.7680.290.5670.77390.3
1.71-1.743.40.42213160.820.2540.4950.82489.6
1.74-1.783.30.37413580.850.2270.440.84789.7
1.78-1.823.30.30813140.8840.1890.3630.79287.4
1.82-1.863.20.24613150.9240.1510.2910.82186.6
1.86-1.93.30.212940.9320.1210.2360.88786.2
1.9-1.963.30.212750.9430.1180.2340.98384.4
1.96-2.013.70.15912830.9650.090.1830.986.4
2.01-2.083.70.12812890.960.0730.1480.8783.8
2.08-2.153.80.1112650.9810.0610.1260.95683.8
2.15-2.243.80.08812520.9880.0480.10.89184
2.24-2.343.70.07512250.9880.0430.0870.88481
2.34-2.463.70.06612430.9910.0370.0760.90781.2
2.46-2.624.20.05612350.9940.0290.0640.83381.9
2.62-2.824.30.04712300.9960.0240.0530.84780.8
2.82-3.114.30.03612550.9980.0190.0410.73782.2
3.11-3.553.90.03113270.9980.0170.0360.79986.3
3.55-4.484.50.0315210.9970.0160.0340.90599
4.48-504.50.0315940.9980.0160.0340.93799.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.638→40.216 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.03
RfactorNum. reflection% reflectionSelection details
Rfree0.1707 1879 4.96 %0.05
Rwork0.1403 ---
obs0.1418 37853 63.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.2 Å2 / Biso mean: 18.9451 Å2 / Biso min: 5.97 Å2
Refinement stepCycle: final / Resolution: 1.638→40.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 68 155 2272
Biso mean--28.48 24.6 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092162
X-RAY DIFFRACTIONf_angle_d1.1092938
X-RAY DIFFRACTIONf_chiral_restr0.059301
X-RAY DIFFRACTIONf_plane_restr0.007381
X-RAY DIFFRACTIONf_dihedral_angle_d15.2331263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6378-1.68210.2809750.22481510158535
1.6821-1.73160.269990.20791922202144
1.7316-1.78750.2144950.18392004209946
1.7875-1.85140.21511110.1632054216547
1.8514-1.92550.19211190.15172221234051
1.9255-2.01310.15981160.14192463257956
2.0131-2.11930.16341520.12632793294564
2.1193-2.2520.13471590.13173163332272
2.252-2.42590.19961670.13653204337174
2.4259-2.670.19871940.14533371356577
2.67-3.05620.1831570.1393348350576
3.0562-3.850.17121970.12943635383284
3.85-40.22760.13862380.13554286452498
Refinement TLS params.Method: refined / Origin x: -9.5968 Å / Origin y: -1.583 Å / Origin z: 16.1351 Å
111213212223313233
T0.0041 Å2-0.0066 Å20.0019 Å2-0.0022 Å20.0083 Å2--0.0026 Å2
L0.0149 °2-0.0071 °20.0014 °2-0.0133 °2-0.0076 °2--0.0107 °2
S-0.0118 Å °-0.0319 Å °0.0225 Å °-0.0254 Å °-0.0113 Å °0.0273 Å °0.0241 Å °0.0044 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allD2 - 150
4X-RAY DIFFRACTION1allD151 - 159
5X-RAY DIFFRACTION1allC1
6X-RAY DIFFRACTION1allE400
7X-RAY DIFFRACTION1allF1

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