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- PDB-6yzr: Carborane nido-butyl-sulfonamide in complex with CA II -

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Basic information

Entry
Database: PDB / ID: 6yzr
TitleCarborane nido-butyl-sulfonamide in complex with CA II
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: 1.2 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
Revision 2.2Oct 1, 2025Group: Derived calculations / Structure summary
Category: pdbx_entry_details / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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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)29,6123
Polymers29,2891
Non-polymers3232
Water5,350297
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 area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.216, 41.374, 71.909
Angle α, β, γ (deg.)90.000, 104.330, 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-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.: 297 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris-H2SO4

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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 PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.2→40.9 Å / Num. obs: 74406 / % possible obs: 98.5 % / Redundancy: 4.647 % / Biso Wilson estimate: 16.778 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.054 / Χ2: 0.842 / Net I/σ(I): 15.24 / Num. measured all: 345758
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
1.2-1.274.5940.5212.485480712139119290.8140.58898.3
1.27-1.364.5120.3593.555091811432112850.8850.40798.7
1.36-1.474.7060.2485.274950010616105180.9490.2899.1
1.47-1.614.580.1478.6144282982396680.9810.16798.4
1.61-1.84.7920.09413.9742259889488180.9930.10699.1
1.8-2.084.6760.05424.0835875783976720.9970.06197.9
2.08-2.544.810.0435.5131661665365830.9980.04598.9
2.54-3.594.6020.02945.2223288520850600.9990.03297.2
3.59-40.94.5830.02353.8713168294928730.9990.02697.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4MDG

4mdg


Resolution: 1.2→40.9 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.34 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0353 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.036
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.162 1089 1.5 %RANDOM
Rwork0.1326 ---
obs0.1331 73358 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 62.84 Å2 / Biso mean: 17.516 Å2 / Biso min: 6.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.07 Å2
2---0.8 Å2-0 Å2
3---0.52 Å2
Refinement stepCycle: final / Resolution: 1.2→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 58 308 2390
Biso mean--18.91 29.75 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192301
X-RAY DIFFRACTIONr_bond_other_d0.0090.022103
X-RAY DIFFRACTIONr_angle_refined_deg1.822.0453331
X-RAY DIFFRACTIONr_angle_other_deg5.67134963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6915290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16424.757103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37415363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.536157
X-RAY DIFFRACTIONr_chiral_restr0.1170.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212534
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02513
X-RAY DIFFRACTIONr_rigid_bond_restr9.77332253
X-RAY DIFFRACTIONr_sphericity_free22.396542
X-RAY DIFFRACTIONr_sphericity_bonded11.80552341
LS refinement shellResolution: 1.2→1.23 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.281 79 -
Rwork0.211 5335 -
obs--97.43 %

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