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- PDB-8aa6: CAII in complex with meta-carboran-propylsulfonamid -

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Basic information

Entry
Database: PDB / ID: 8aa6
TitleCAII in complex with meta-carboran-propylsulfonamid
ComponentsCarbonic anhydrase 2
KeywordsHYDROLASE / Inhibitor / Complex / Carbonicanhydrase
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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
meta-carboran-propylsulfonamid / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsBrynda, J. / Rezacova, P. / Kugler, M.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Technology Agency of the Czech RepublicTE01020028 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0/16_019/0000868 Czech Republic
CitationJournal: Phys Chem Chem Phys / Year: 2023
Title: B-H⋯ pi and C-H⋯ pi interactions in protein-ligand complexes: carbonic anhydrase II inhibition by carborane sulfonamides.
Authors: Fanfrlik, J. / Brynda, J. / Kugler, M. / Lepsik, M. / Pospisilova, K. / Holub, J. / Hnyk, D. / Nekvinda, J. / Gruner, B. / Rezacova, P.
History
DepositionJun 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,6093
Polymers29,2891
Non-polymers3202
Water4,179232
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)42.172, 41.432, 72.165
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-LD3 / meta-carboran-propylsulfonamid


Mass: 254.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8B10NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.09 Å3/Da / Density % sol: 41.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 50 mM Tris 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: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.14→40.89 Å / Num. obs: 86327 / % possible obs: 98.4 % / Redundancy: 3.654 % / Biso Wilson estimate: 18.711 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.051 / Χ2: 0.828 / Net I/σ(I): 12.47 / Num. measured all: 315480
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
1.14-1.213.4720.871.194689614091135060.531.02695.8
1.21-1.293.7170.4642.394893313262131650.8240.54399.3
1.29-1.43.5630.2434.344335012354121670.9390.28698.5
1.4-1.533.8080.1338.134309111387113170.9820.15599.4
1.53-1.713.6270.08213.453678110309101410.9920.09698.4
1.71-1.983.8560.05121.8235143914391140.9970.05999.7
1.98-2.423.5920.03928.827167772275630.9970.04597.9
2.42-3.423.730.03334.4922381602860000.9980.03899.5
3.42-40.893.50.02936.9511738342133540.9980.03598

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YZT

6yzt


Resolution: 1.15→40.89 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.279 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0367 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1805 1761 2.1 %RANDOM
Rwork0.1617 ---
obs0.162 83156 98.86 %-
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: 66.13 Å2 / Biso mean: 21.202 Å2 / Biso min: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.25 Å2
2--0.05 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.15→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 20 238 2298
Biso mean--23.7 31.47 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132208
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172023
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.73094
X-RAY DIFFRACTIONr_angle_other_deg1.4221.6094732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1995273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38923.868106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36715363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.692157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022496
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02482
X-RAY DIFFRACTIONr_rigid_bond_restr2.02834231
LS refinement shellResolution: 1.15→1.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 128 -
Rwork0.388 6102 -
all-6230 -
obs--98.22 %

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