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- PDB-9qq3: Crystal structure of human carbonic anhydrase VII in complex with... -

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Basic information

Entry
Database: PDB / ID: 9qq3
TitleCrystal structure of human carbonic anhydrase VII in complex with a benzenesufonamide derivative containing the duloxetine moiety
ComponentsCarbonic anhydrase 7
KeywordsLYASE / 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: 1.6 Å
AuthorsD'Ambrosio, K. / Di Fiore, A. / 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)31,6383
Polymers30,9261
Non-polymers7122
Water2,828157
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 area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.455, 89.671, 44.442
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: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1I9C / [4-[(4-sulfamoylphenyl)carbamothioylamino]phenyl] ~{N}-methyl-~{N}-[(3~{S})-3-naphthalen-1-yloxy-3-thiophen-2-yl-propyl]carbamate


Mass: 646.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H30N4O5S3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 8% 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 PILATUS 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: 1.6→50 Å / Num. obs: 35953 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.03 / Rrim(I) all: 0.105 / Χ2: 1.027 / Net I/σ(I): 9.3 / Num. measured all: 433280
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.6-1.6311.40.72217500.8780.9670.2250.7570.994100
1.63-1.66120.67417780.9040.9750.2030.7050.994100
1.66-1.6912.20.61717420.9180.9780.1850.6451.011100
1.69-1.7211.40.51217800.9320.9820.1590.5371.014100
1.72-1.76120.42617790.9530.9880.1280.4450.996100
1.76-1.812.30.37117630.9680.9920.110.3870.996100
1.8-1.8512.10.31517930.9760.9940.0950.331.04100
1.85-1.911.90.29117610.9670.9920.0880.3051.013100
1.9-1.9511.30.32217870.920.9790.1010.3380.992100
1.95-2.0212.20.19117770.9890.9970.0570.21.086100
2.02-2.09120.19417870.9850.9960.0590.2031.062100
2.09-2.1711.60.14117670.9930.9980.0430.1470.992100
2.17-2.2712.50.18818030.9810.9950.0550.1971.004100
2.27-2.3912.60.12117890.9950.9990.0350.1260.993100
2.39-2.5412.50.10517970.9960.9990.0310.111.069100
2.54-2.7412.50.09518140.9970.9990.0280.0991.074100
2.74-3.0112.20.07918190.9970.9990.0240.0831.01100
3.01-3.45130.06918300.9980.9990.020.0711.129100
3.45-4.34120.05718580.99810.0170.0590.992100
4.34-5011.40.05719790.9970.9990.0180.061.06399.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
SCALEPACKdata scaling
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→44.48 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.684 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22388 2084 5.8 %RANDOM
Rwork0.18672 ---
obs0.1889 33700 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.023 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.83 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.6→44.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 45 157 2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122203
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.8373001
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2595266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.318514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09310342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1290.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021760
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.0451.8161055
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9893.2581324
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7652.3961148
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.58626.813303
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.639 Å
RfactorNum. reflection% reflection
Rfree0.241 153 -
Rwork0.202 2397 -
obs--97.51 %

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