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- PDB-6z04: Nido-carborane butyl-sulfonamide in complex with CA IX mimic -

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Basic information

Entry
Database: PDB / ID: 6z04
TitleNido-carborane butyl-sulfonamide in complex with CA IX mimic
ComponentsCarbonic anhydrase 2
KeywordsLYASE / CARBONIC ANHYDRASE / CA INHIBITOR
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 / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / 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 / cytoplasm / 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
Carborane nido-butyl-sulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsKugler, M. / Brynda, J. / Pospisilova, K. / Rezacova, P.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science FoundationGA15-05677S Czech Republic
Other governmentTE01020028 Czech Republic
CitationJournal: J Enzyme Inhib Med Chem / Year: 2020
Title: The structural basis for the selectivity of sulfonamido dicarbaboranes toward cancer-associated carbonic anhydrase IX.
Authors: Kugler, M. / Holub, J. / Brynda, J. / Pospisilova, K. / Anwar, S.E. / Bavol, D. / Havranek, M. / Kral, V. / Fabry, M. / Gruner, B. / Rezacova, P.
History
DepositionMay 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 4, 2020Group: Non-polymer description / Structure summary / Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5243
Polymers29,2011
Non-polymers3232
Water5,098283
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.035, 41.345, 72.682
Angle α, β, γ (deg.)90.000, 103.980, 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: 29200.887 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-Q3W / Carborane nido-butyl-sulfonamide


Mass: 257.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10B9NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 50 mM Tris pH=7.8 1.6 M Natrium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.05→40.79 Å / Num. obs: 111433 / % possible obs: 97.8 % / Redundancy: 3.258 % / Biso Wilson estimate: 13.945 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.082 / Χ2: 1.05 / Net I/σ(I): 7.9 / Num. measured all: 363069
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.05-1.113.0810.8351.125351118355173690.4671.0194.6
1.11-1.193.2470.432.435520217203170000.7880.51698.8
1.19-1.283.2380.273.695113216087157920.9040.32398.2
1.28-1.43.3650.1725.734920714782146240.9590.20598.9
1.4-1.573.30.1148.614320313352130900.9810.13698
1.57-1.813.4270.08212.944039211856117870.990.09799.4
1.81-2.223.1820.06316.82310541004297590.9920.07597.2
2.22-3.133.3070.05520.0925533781477220.9940.06698.8
3.13-40.793.2250.04621.6213835441642900.9960.05497.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5OGP

5ogp


Resolution: 1.05→40.79 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.929 / SU ML: 0.021 / SU R Cruickshank DPI: 0.0252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1578 2101 1.9 %RANDOM
Rwork0.1408 ---
obs0.1412 109331 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 63.11 Å2 / Biso mean: 15.626 Å2 / Biso min: 7.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å2-0.03 Å2
2---0.09 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 1.05→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 20 286 2316
Biso mean--18.85 26.82 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192342
X-RAY DIFFRACTIONr_bond_other_d0.0070.022123
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9773285
X-RAY DIFFRACTIONr_angle_other_deg2.39434966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9975310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73324.862109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.53515364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.118158
X-RAY DIFFRACTIONr_chiral_restr0.1070.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212703
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02539
X-RAY DIFFRACTIONr_rigid_bond_restr2.28431874
X-RAY DIFFRACTIONr_sphericity_free13.7785166
X-RAY DIFFRACTIONr_sphericity_bonded6.7751948
LS refinement shellResolution: 1.05→1.075 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.361 141 -
Rwork0.354 7353 -
obs--89.27 %

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