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- PDB-6yzs: Carborane closo-pentyl-sulfonamide in complex with CA II -

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Basic information

Entry
Database: PDB / ID: 6yzs
TitleCarborane closo-pentyl-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 / 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 / cyanamide hydratase activity / 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 / 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-pentyl-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 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)29,6604
Polymers29,2891
Non-polymers3713
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.045, 41.301, 72.024
Angle α, β, γ (deg.)90.000, 104.310, 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-Q3N / Carborane closo-pentyl-sulfonamide


Mass: 282.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12B10NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.07 Å3/Da / Density % sol: 40.55 %
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: Jan 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.05→40.74 Å / Num. obs: 106217 / % possible obs: 94.7 % / Redundancy: 4.851 % / Biso Wilson estimate: 14.204 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.056 / Χ2: 1.181 / Net I/σ(I): 14.4 / Num. measured all: 515231
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
1.05-1.114.6760.8931.557516818062160760.6981.00289
1.11-1.194.9120.522.827752516938157820.8630.58193.2
1.19-1.284.810.3574.147168415796149040.930.494.4
1.28-1.415.1680.236.767166914553138690.9730.25595.3
1.41-1.574.8640.13411.266181313182127080.9890.1596.4
1.57-1.824.8430.07420.595487611647113300.9960.08397.3
1.82-2.224.960.04235.6348054989796880.9980.04797.9
2.22-3.144.4460.03244.9333650768775680.9990.03698.5
3.14-40.744.8440.02456.5920792434542920.9990.02798.8

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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: 1.05→40.74 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.13 / SU ML: 0.024 / SU R Cruickshank DPI: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.029
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 1116 1.1 %RANDOM
Rwork0.1384 ---
obs0.1387 105091 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.02 Å2 / Biso mean: 17.756 Å2 / Biso min: 7.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-0.16 Å2
2---0.53 Å2-0 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 1.05→40.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 44 367 2441
Biso mean--29.13 29.82 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192285
X-RAY DIFFRACTIONr_bond_other_d0.0070.022067
X-RAY DIFFRACTIONr_angle_refined_deg1.82.0333298
X-RAY DIFFRACTIONr_angle_other_deg4.10334866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8885288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01824.66103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26315359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.843158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212536
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02509
X-RAY DIFFRACTIONr_rigid_bond_restr6.90832211
X-RAY DIFFRACTIONr_sphericity_free24.345552
X-RAY DIFFRACTIONr_sphericity_bonded14.59652373
LS refinement shellResolution: 1.05→1.076 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.264 75 -
Rwork0.281 7016 -
obs--85.75 %

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