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- PDB-6sds: HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH A SULFONAMIDE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 6sds
TitleHUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH A SULFONAMIDE INHIBITOR
ComponentsCarbonic anhydrase 2
KeywordsLYASE / CARBONIC ANHYDRASE II / ZINC ENZYME / SULFONAMIDE INHIBITOR
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 / 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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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, 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
Similarity search - Domain/homology
phenyl-(4-sulfamoylphenoxy)phosphinic acid / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.26 Å
AuthorsAlterio, V. / De Simone, G. / Esposito, D.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Phenyl(thio)phosphon(amid)ate Benzenesulfonamides as Potent and Selective Inhibitors of Human Carbonic Anhydrases II and VII Counteract Allodynia in a Mouse Model of Oxaliplatin-Induced Neuropathy.
Authors: Nocentini, A. / Alterio, V. / Bua, S. / Micheli, L. / Esposito, D. / Buonanno, M. / Bartolucci, G. / Osman, S.M. / ALOthman, Z.A. / Cirilli, R. / Pierini, M. / Monti, S.M. / Di Cesare ...Authors: Nocentini, A. / Alterio, V. / Bua, S. / Micheli, L. / Esposito, D. / Buonanno, M. / Bartolucci, G. / Osman, S.M. / ALOthman, Z.A. / Cirilli, R. / Pierini, M. / Monti, S.M. / Di Cesare Mannelli, L. / Gratteri, P. / Ghelardini, C. / De Simone, G. / Supuran, C.T.
History
DepositionJul 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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)29,7464
Polymers29,2891
Non-polymers4573
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint2 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.224, 41.241, 71.946
Angle α, β, γ (deg.)90.000, 104.110, 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: 29289.062 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-L8N / phenyl-(4-sulfamoylphenoxy)phosphinic acid


Mass: 313.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12NO5PS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


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


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.3 M SODIUM CITRATE, 60 mM TRIS-HCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 21, 2018
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.26→35.5 Å / Num. obs: 64217 / % possible obs: 98.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.028 / Rrim(I) all: 0.061 / Χ2: 1.035 / Net I/σ(I): 23.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.26-1.281.80.39925210.7730.2920.4980.9977.6
1.28-1.312.40.35531230.8370.2390.4311.06597.3
1.31-1.332.60.34131910.8460.220.4091.04698.2
1.33-1.362.80.32431960.8760.2030.3851.04499.5
1.36-1.392.90.29832580.8880.1850.3541.0599.6
1.39-1.4230.25432240.9240.1540.2991.09799.7
1.42-1.453.10.2332120.9430.1390.271.07499.3
1.45-1.493.20.19332170.9580.1160.2271.07999.4
1.49-1.543.30.16732430.9720.0980.1941.08299.6
1.54-1.593.40.13832480.980.080.1611.09299.6
1.59-1.643.60.12232430.9820.070.1421.09199.8
1.64-1.713.70.1132360.9860.0620.1271.06699.9
1.71-1.793.90.09132750.990.050.1041.014100
1.79-1.884.10.07832420.9920.0420.0891.04100
1.88-24.30.06832670.9930.0360.0771.015100
2-2.154.60.06232490.9940.0320.071.044100
2.15-2.374.90.05632980.9950.0280.0630.979100
2.37-2.715.10.05232750.9960.0260.0580.936100
2.71-3.425.30.04133160.9980.0190.0450.977100
3.42-35.55.60.03133830.9990.0140.0341.06399.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
CrystalCleardata collection
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6H29

6h29


Resolution: 1.26→35.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.212 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.043
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1741 1066 1.7 %RANDOM
Rwork0.1462 ---
obs0.1467 63136 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 51.97 Å2 / Biso mean: 11.079 Å2 / Biso min: 4.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-0.01 Å2
2--0.11 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: final / Resolution: 1.26→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 25 190 2287
Biso mean--13.66 18.49 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132216
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171980
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.643012
X-RAY DIFFRACTIONr_angle_other_deg1.5061.5974633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7475272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96723.796108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.54415365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.988157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02451
X-RAY DIFFRACTIONr_rigid_bond_restr1.73834196
LS refinement shellResolution: 1.26→1.291 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.245 52 -
Rwork0.202 3795 -
obs--80.65 %

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