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- PDB-6yzx: Carborane nido-hexyl-sulfonamide in complex with CA II -

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Basic information

Entry
Database: PDB / ID: 6yzx
TitleCarborane nido-hexyl-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 nido-hexyl-sulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 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)29,6403
Polymers29,2891
Non-polymers3512
Water4,396244
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 area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.150, 41.340, 72.350
Angle α, β, γ (deg.)90.000, 104.440, 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-Q3H / Carborane nido-hexyl-sulfonamide


Mass: 285.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14B9NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 40.98 %
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: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.09→35.6 Å / Num. obs: 93252 / % possible obs: 92.4 % / Redundancy: 3.841 % / Biso Wilson estimate: 15.822 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.06 / Χ2: 1.086 / Net I/σ(I): 10.93 / Num. measured all: 358193
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
1.09-1.163.7310.9311.184778416220128070.531.08479
1.16-1.243.9080.6211.895510615270141010.7210.71892.3
1.24-1.333.7290.4162.784924714194132070.8360.48593
1.33-1.464.0340.2664.625061913106125470.9340.30795.7
1.46-1.633.9250.1418.394494311869114510.9820.16396.5
1.63-1.893.70.07614.79367311047899270.9940.08994.7
1.89-2.313.9720.04327.0334640890387210.9980.04998
2.31-3.263.6380.03134.7624265693366700.9980.03796.2
3.26-35.63.8890.02845.0714858391138210.9990.03397.7

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Processing

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

4mdg


Resolution: 1.1→35.6 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.1676 / WRfactor Rwork: 0.1439 / FOM work R set: 0.8774 / SU B: 1.175 / SU ML: 0.024 / SU R Cruickshank DPI: 0.0303 / SU Rfree: 0.0307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1656 1831 2 %RANDOM
Rwork0.1431 ---
obs0.1435 89695 93.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 57.53 Å2 / Biso mean: 17.428 Å2 / Biso min: 7.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0.21 Å2
2---0.09 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 1.1→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 43 255 2333
Biso mean--22.32 26.93 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192237
X-RAY DIFFRACTIONr_bond_other_d0.0050.022057
X-RAY DIFFRACTIONr_angle_refined_deg1.6352.0163165
X-RAY DIFFRACTIONr_angle_other_deg1.53734809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93224.902102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90515359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.052157
X-RAY DIFFRACTIONr_chiral_restr0.1110.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212477
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02500
X-RAY DIFFRACTIONr_rigid_bond_restr4.54232234
X-RAY DIFFRACTIONr_sphericity_free16.992547
X-RAY DIFFRACTIONr_sphericity_bonded9.04252302
LS refinement shellResolution: 1.1→1.128 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 114 -
Rwork0.278 5599 -
all-5713 -
obs--79.07 %

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