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- PDB-9qq2: Crystal structure of human carbonic anhydrase VII in complex with... -

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Basic information

Entry
Database: PDB / ID: 9qq2
TitleCrystal structure of human carbonic anhydrase VII in complex with a benzenesulfonamide derivative containing the duloxetine moiety.
ComponentsCarbonic anhydrase 7
KeywordsLYASE / Protein-inhibitor complex / Duloxetine / Neuropathic pain / Carbonic Anhydrase VII
Function / homology
Function and homology information


: / regulation of chloride transport / Reversible hydration of carbon dioxide / carbonic anhydrase / regulation of intracellular pH / carbonate dehydratase activity / positive regulation of synaptic transmission, GABAergic / neuron cellular homeostasis / zinc ion binding / cytoplasm / cytosol
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
: / Carbonic anhydrase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.35 Å
AuthorsDi Fiore, A. / D'Ambrosio, K. / De Simone, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Multimodal Neuropathic Pain Management: Novel Approaches Through Inhibition of the Carbonic Anhydrase Enzymes
Authors: Angeli, A. / Rosi, G. / Micheli, L. / D'Ambrosio, K. / Di Fiore, A. / Ghelardini, C. / Di Cesare Mannelli, L. / Bartolucci, G. / Carta, F. / De Simone, G. / Papini, A.M. / Supuran, C.T.
History
DepositionMar 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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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)31,5173
Polymers30,9261
Non-polymers5912
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.656, 89.866, 44.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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
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: isolated from a natural source / Formula: Zn
#3: Chemical ChemComp-A1I9B / 1-methyl-1-[(3~{S})-3-naphthalen-1-yloxy-3-thiophen-2-yl-propyl]-3-[(4-sulfamoylphenyl)methyl]thiourea


Mass: 525.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27N3O3S3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% w/v Peg 3350, 0.2 M Ammonium acetate and 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 57576 / % possible obs: 97.1 % / Redundancy: 12 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Χ2: 1.047 / Net I/σ(I): 9.8 / Num. measured all: 689844
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.35-1.3711.40.63929000.8990.9730.1990.6710.992100
1.37-1.412.10.57329410.9310.9820.1720.5990.998100
1.4-1.4311.80.52229120.930.9820.1590.5471.03799.9
1.43-1.4511.90.48828800.9340.9830.1480.511.09899.2
1.45-1.4912.40.41629460.9590.990.1230.4341.08100
1.49-1.5212.30.34629350.9680.9920.1030.3611.024100
1.52-1.5612.10.29629100.9740.9930.0890.311.054100
1.56-1.611.60.25829450.9750.9940.0790.271.048100
1.6-1.6512.20.22929310.9840.9960.0680.2391.06100
1.65-1.712.20.229620.9840.9960.060.2091.062100
1.7-1.7611.80.17429010.9880.9970.0520.1821.08799
1.76-1.8312.70.15529540.9910.9980.0450.1621.068100
1.83-1.9211.50.14126380.970.9920.0450.1491.04689.1
1.92-2.02110.11827930.9920.9980.0360.1231.03594.4
2.02-2.1412.20.10429630.9950.9990.0310.1081.065100
2.14-2.3111.40.09521910.9960.9990.0290.0991.09773.7
2.31-2.5412.80.08229710.9970.9990.0240.0861.0499.6
2.54-2.9112.80.06830150.99810.020.0711.009100
2.91-3.6611.90.05328800.99810.0160.0551.03394.1
3.66-5011.50.03830080.99910.0120.041.01993.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
SCALEPACKdata scaling
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.35→44.4 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.338 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18906 2008 3.5 %RANDOM
Rwork0.15315 ---
obs0.15433 55491 96.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20 Å2
2--0.62 Å20 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.35→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 36 198 2288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122181
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161961
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.822970
X-RAY DIFFRACTIONr_angle_other_deg0.7071.7794537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.036513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32210339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02525
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1171.4011050
X-RAY DIFFRACTIONr_mcbond_other5.0981.41050
X-RAY DIFFRACTIONr_mcangle_it7.482.5241316
X-RAY DIFFRACTIONr_mcangle_other7.4842.5261317
X-RAY DIFFRACTIONr_scbond_it7.1431.7641131
X-RAY DIFFRACTIONr_scbond_other7.141.7661132
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.2213.071655
X-RAY DIFFRACTIONr_long_range_B_refined12.0994096.872427
X-RAY DIFFRACTIONr_long_range_B_other12.1714171.742383
X-RAY DIFFRACTIONr_rigid_bond_restr4.23734076
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 158 -
Rwork0.203 4089 -
obs--97.9 %

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