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- PDB-7zl5: Azosemide in complex with Carbonic Anhydrase I -

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Basic information

Entry
Database: PDB / ID: 7zl5
TitleAzosemide in complex with Carbonic Anhydrase I
ComponentsCarbonic anhydrase 1
KeywordsLYASE / carbonic anhydrase / inhibitor / metalloenzyme / azosemide / loop diuretic
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / extracellular exosome / zinc ion binding / cytosol
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
Azosemide / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.479 Å
AuthorsAngeli, A. / Ferraroni, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Struct. / Year: 2022
Title: Sulfonamide diuretic azosemide as an efficient carbonic anhydrase inhibitor
Authors: Ferraroni, M. / Angeli, A. / Pinteala, M. / Supuran, C.T.
History
DepositionApr 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Carbonic anhydrase 1
BBB: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7637
Polymers57,8122
Non-polymers9515
Water6,720373
1
AAA: Carbonic anhydrase 1
hetero molecules


  • defined by author
  • 29.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)29,4214
Polymers28,9061
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Carbonic anhydrase 1
hetero molecules


  • defined by author
  • 29.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)29,3423
Polymers28,9061
Non-polymers4362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.230, 71.780, 120.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbonic anhydrase 1 / Carbonate dehydratase I / Carbonic anhydrase B / CAB / Carbonic anhydrase I / CA-I


Mass: 28906.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00915, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-IWE / Azosemide / 2-chloranyl-5-(1~{H}-1,2,3,4-tetrazol-5-yl)-4-(thiophen-2-ylmethylamino)benzenesulfonamide


Mass: 370.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H11ClN6O2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 28-31% PEG4000, 0.2 M Sodium acetate, 0.1 M Tris pH 8.5-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9717 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 1.479→46.289 Å / Num. obs: 92506 / % possible obs: 100 % / Redundancy: 12.48 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.052 / Net I/σ(I): 24.43
Reflection shellResolution: 1.479→1.52 Å / Redundancy: 12.35 % / Rmerge(I) obs: 1.232 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 6748 / CC1/2: 0.872 / Rrim(I) all: 1.286 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JV0

1jv0


Resolution: 1.479→46.289 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.592 / SU ML: 0.057 / Cross valid method: NONE / ESU R: 0.07 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2139 4583 4.954 %
Rwork0.1843 87922 -
all0.186 --
obs-92505 99.948 %
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: 25.308 Å2
Baniso -1Baniso -2Baniso -3
1--0.529 Å20 Å20 Å2
2--1.87 Å2-0 Å2
3----1.341 Å2
Refinement stepCycle: LAST / Resolution: 1.479→46.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 52 373 4441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134211
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153791
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.6395743
X-RAY DIFFRACTIONr_angle_other_deg1.4641.5868783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19423.707205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34315665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4071514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025009
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02963
X-RAY DIFFRACTIONr_nbd_refined0.2050.2796
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.23648
X-RAY DIFFRACTIONr_nbtor_refined0.170.22018
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2272
X-RAY DIFFRACTIONr_metal_ion_refined0.0650.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.210
X-RAY DIFFRACTIONr_nbd_other0.1930.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.214
X-RAY DIFFRACTIONr_mcbond_it2.2082.4412056
X-RAY DIFFRACTIONr_mcbond_other2.2042.442055
X-RAY DIFFRACTIONr_mcangle_it3.0033.6582575
X-RAY DIFFRACTIONr_mcangle_other3.0053.662570
X-RAY DIFFRACTIONr_scbond_it3.5882.7652155
X-RAY DIFFRACTIONr_scbond_other3.5782.7652155
X-RAY DIFFRACTIONr_scangle_it5.1244.0113163
X-RAY DIFFRACTIONr_scangle_other5.1294.0123164
X-RAY DIFFRACTIONr_lrange_it6.08429.684662
X-RAY DIFFRACTIONr_lrange_other6.07829.6744662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.479-1.5170.3143330.2986411X-RAY DIFFRACTION99.8963
1.517-1.5590.2723400.2726248X-RAY DIFFRACTION99.9242
1.559-1.6040.2773180.2536107X-RAY DIFFRACTION99.9844
1.604-1.6530.2623200.2325915X-RAY DIFFRACTION99.984
1.653-1.7080.2563230.2215745X-RAY DIFFRACTION99.967
1.708-1.7670.2622860.2085558X-RAY DIFFRACTION99.9487
1.767-1.8340.2312710.2035358X-RAY DIFFRACTION99.929
1.834-1.9090.2272650.1975182X-RAY DIFFRACTION99.9083
1.909-1.9940.2412710.1974985X-RAY DIFFRACTION99.981
1.994-2.0910.2272240.24776X-RAY DIFFRACTION100
2.091-2.2040.2372210.1994574X-RAY DIFFRACTION99.9375
2.204-2.3370.22150.1864317X-RAY DIFFRACTION99.9559
2.337-2.4980.2182100.1754032X-RAY DIFFRACTION100
2.498-2.6980.2281910.1753787X-RAY DIFFRACTION99.9497
2.698-2.9550.1961920.183481X-RAY DIFFRACTION99.9456
2.955-3.3030.2151590.1793192X-RAY DIFFRACTION99.9702
3.303-3.8120.2171480.1742827X-RAY DIFFRACTION99.9664
3.812-4.6650.1551360.1412391X-RAY DIFFRACTION99.9209
4.665-6.5780.175990.1591910X-RAY DIFFRACTION99.9006
6.578-46.2890.213610.1771126X-RAY DIFFRACTION99.6641

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