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- PDB-6yzq: Carborane closo-butyl-sulfonamide in complex with CA II -

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Basic information

Entry
Database: PDB / ID: 6yzq
TitleCarborane closo-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 / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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 / one-carbon metabolic process / 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
Carborane closo-butyl-sulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.04 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 1.1Jan 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)29,6233
Polymers29,2891
Non-polymers3342
Water5,945330
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 area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.114, 41.394, 72.157
Angle α, β, γ (deg.)90.000, 104.430, 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-Q3Q / Carborane closo-butyl-sulfonamide


Mass: 268.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10B10NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
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: Sep 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.04→40.79 Å / Num. obs: 106505 / % possible obs: 93.3 % / Redundancy: 4.172 % / Biso Wilson estimate: 13.468 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.077 / Χ2: 0.733 / Net I/σ(I): 10.64 / Num. measured all: 444323
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
1.04-1.114.0140.7791.76270418370156220.5650.89285
1.11-1.184.230.5172.986830617275161470.7910.58993.5
1.18-1.284.1380.3944.026252716122151100.8780.44993.7
1.28-1.44.2950.2626.136043914792140730.9490.29795.1
1.4-1.574.1980.1599.465330813435126970.9810.18194.5
1.57-1.814.3350.09315.834984111871114970.9930.10696.8
1.81-2.214.0420.05723.53384251004795060.9960.06594.6
2.21-3.134.1410.04230.7731726782776620.9980.04897.9
3.13-40.794.0680.03635.7617047442341910.9980.04294.8

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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: 1.04→40.79 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.376 / SU ML: 0.028 / SU R Cruickshank DPI: 0.0262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1596 1118 1.1 %RANDOM
Rwork0.141 ---
obs0.1412 105334 93.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.83 Å2 / Biso mean: 18.645 Å2 / Biso min: 9.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0 Å21.13 Å2
2---0.61 Å20 Å2
3---0.72 Å2
Refinement stepCycle: final / Resolution: 1.04→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 41 355 2427
Biso mean--18.71 29.13 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192239
X-RAY DIFFRACTIONr_bond_other_d0.0070.022042
X-RAY DIFFRACTIONr_angle_refined_deg1.82.0333224
X-RAY DIFFRACTIONr_angle_other_deg4.62634801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41224.851101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67715354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.913157
X-RAY DIFFRACTIONr_chiral_restr0.1210.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212487
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02502
X-RAY DIFFRACTIONr_rigid_bond_restr4.0932206
X-RAY DIFFRACTIONr_sphericity_free23.188581
X-RAY DIFFRACTIONr_sphericity_bonded15.17452372
LS refinement shellResolution: 1.044→1.072 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 67 -
Rwork0.338 6357 -
all-6424 -
obs--76.27 %

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