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- PDB-9gu7: Human carbonic anhydrase II complexed with N-phenyl-2-(1H-tetrazo... -

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Basic information

Entry
Database: PDB / ID: 9gu7
TitleHuman carbonic anhydrase II complexed with N-phenyl-2-(1H-tetrazol-5-yl)acetamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / tetrazole / carbonic anhydrase II / inhibitor / metalloenzyme
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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / 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
: / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsAngeli, A. / Ferraroni, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Tetrazole Is a Novel Zinc Binder Chemotype for Carbonic Anhydrase Inhibition.
Authors: Giovannuzzi, S. / Angeli, A. / Begines, P. / Ferraroni, M. / Nocentini, A. / Supuran, C.T.
History
DepositionSep 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6204
Polymers29,2891
Non-polymers3313
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint3 kcal/mol
Surface area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.455, 41.681, 72.709
Angle α, β, γ (deg.)90.000, 104.603, 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-A1IOX / N-phenyl-2-(1H-tetrazol-5-yl)acetamide / ~{N}-phenyl-2-(1~{H}-1,2,3,4-tetrazol-5-yl)ethanamide


Mass: 203.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5 M sodium citrate, 0.1 M Tris pH 8.0

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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: Jun 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→35.89 Å / Num. obs: 48117 / % possible obs: 88.8 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.047 / Net I/σ(I): 22.6
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1325 / CC1/2: 0.788 / Rrim(I) all: 0.51 / % possible all: 50.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→35.89 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.76 / SU ML: 0.032 / Cross valid method: NONE / ESU R: 0.056 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.165 2414 5.036 %
Rwork0.1223 45522 -
all0.124 --
obs-47936 88.34 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.815 Å2-0 Å20.055 Å2
2--0.238 Å2-0 Å2
3---0.483 Å2
Refinement stepCycle: LAST / Resolution: 1.35→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 20 286 2362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132195
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171991
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.6382990
X-RAY DIFFRACTIONr_angle_other_deg1.5241.5914665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0465276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81523.853109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46315368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.116157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022502
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02450
X-RAY DIFFRACTIONr_nbd_refined0.2390.2408
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21872
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21005
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21031
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2186
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.340.218
X-RAY DIFFRACTIONr_nbd_other0.2020.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.229
X-RAY DIFFRACTIONr_mcbond_it2.7171.3971053
X-RAY DIFFRACTIONr_mcbond_other2.4161.3881052
X-RAY DIFFRACTIONr_mcangle_it3.012.1011319
X-RAY DIFFRACTIONr_mcangle_other3.112.1071320
X-RAY DIFFRACTIONr_scbond_it6.0191.7731142
X-RAY DIFFRACTIONr_scbond_other6.0161.7731143
X-RAY DIFFRACTIONr_scangle_it6.5382.5031662
X-RAY DIFFRACTIONr_scangle_other6.5362.5041663
X-RAY DIFFRACTIONr_lrange_it4.79317.8552476
X-RAY DIFFRACTIONr_lrange_other4.69317.152408
X-RAY DIFFRACTIONr_rigid_bond_restr4.55334186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3850.2581010.1942215X-RAY DIFFRACTION58.5144
1.385-1.4230.1861680.1433265X-RAY DIFFRACTION88.0708
1.423-1.4640.2691620.2082989X-RAY DIFFRACTION83.5587
1.464-1.5090.2651590.1752936X-RAY DIFFRACTION84.4014
1.509-1.5590.151610.12909X-RAY DIFFRACTION85.9463
1.559-1.6130.1611770.0813246X-RAY DIFFRACTION99.0165
1.613-1.6740.1431730.0783126X-RAY DIFFRACTION99.3675
1.674-1.7430.1581530.0822667X-RAY DIFFRACTION88.1801
1.743-1.820.1361590.0822930X-RAY DIFFRACTION99.6773
1.82-1.9090.1571240.1182414X-RAY DIFFRACTION86.2385
1.909-2.0120.1751090.1492033X-RAY DIFFRACTION76.8844
2.012-2.1340.151130.1042264X-RAY DIFFRACTION88.9263
2.134-2.2810.1481070.1332118X-RAY DIFFRACTION89.7539
2.281-2.4640.1521190.112207X-RAY DIFFRACTION99.5719
2.464-2.6990.1591000.1091882X-RAY DIFFRACTION92.2719
2.699-3.0160.151910.1171860X-RAY DIFFRACTION99.8976
3.016-3.4820.155750.1231545X-RAY DIFFRACTION93.318
3.482-4.2620.171630.1281228X-RAY DIFFRACTION87.7634
4.262-6.0160.165650.141074X-RAY DIFFRACTION99.65
6.016-35.890.185350.172614X-RAY DIFFRACTION99.2355

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