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- PDB-6sdt: HUMAN CARBONIC ANHYDRASE VII IN COMPLEX WITH A SULFONAMIDE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 6sdt
TitleHUMAN CARBONIC ANHYDRASE VII IN COMPLEX WITH A SULFONAMIDE INHIBITOR
ComponentsCarbonic anhydrase 7
KeywordsLYASE / CARBONIC ANHYDRASE VII / ZINC ENZYME / INHIBITOR / SULFONAMIDE
Function / homology
Function and homology information


positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / one-carbon metabolic process / zinc ion binding ...positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / one-carbon metabolic process / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase VII / 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 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.94 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3043
Polymers30,9261
Non-polymers3792
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.280, 89.360, 44.165
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Carbonic anhydrase 7 / Carbonate dehydratase VII / Carbonic anhydrase VII / CA-VII


Mass: 30925.693 Da / Num. of mol.: 1 / Mutation: C183S and C217S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P43166, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% (W/V) POLYETHYLENE GLYCOL 3350, 0.2 M AMMONIUM ACETATE, 0.1 M 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: Feb 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.94→33.99 Å / Num. obs: 20119 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.037 / Rrim(I) all: 0.092 / Χ2: 1.024 / Net I/av σ(I): 16.493 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.94-1.973.60.5399690.7540.3210.631.02799.8
1.97-2.013.60.4689910.8170.2780.5470.9599.6
2.01-2.053.70.4039700.8550.2350.4691.006100
2.05-2.093.80.38510000.8420.2220.4461.023100
2.09-2.143.90.3199820.9180.1830.3690.98899.9
2.14-2.184.10.2959930.9180.1650.3391.09100
2.18-2.244.50.2649710.9320.1390.31.08299.7
2.24-2.34.90.24210120.9450.1220.2721.11299.9
2.3-2.375.30.21510030.960.1030.2391.092100
2.37-2.445.40.1989880.9650.0940.221.017100
2.44-2.535.60.1769800.9740.0820.1951.088100
2.53-2.635.80.15510170.9780.0710.1721.078100
2.63-2.756.10.1329980.9880.0590.1451.04199.9
2.75-2.96.60.11510030.9920.0490.1251.045100
2.9-3.087.40.09710130.9940.0380.1040.972100
3.08-3.328.70.07910210.9970.0290.0840.951100
3.32-3.658.70.06410080.9980.0230.0681.022100
3.65-4.188.60.04710340.9990.0170.050.963100
4.18-5.268.50.0410500.9990.0150.0431.064100
5.26-33.997.80.03811160.9990.0140.0410.98599.3

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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: 6G4T

6g4t


Resolution: 1.94→33.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.331 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.15 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1010 5 %RANDOM
Rwork0.1877 ---
obs0.1896 19072 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.51 Å2 / Biso mean: 20.985 Å2 / Biso min: 6.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0 Å20 Å2
2--0.75 Å2-0 Å2
3----0.29 Å2
Refinement stepCycle: final / Resolution: 1.94→33.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 21 94 2169
Biso mean--20.35 22.35 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122144
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.6272911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07121.786112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9315335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1921513
X-RAY DIFFRACTIONr_chiral_restr0.1260.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021698
LS refinement shellResolution: 1.94→1.988 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.258 61 -
Rwork0.212 1356 -
obs--97.86 %

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