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- PDB-5lmd: The crystal structure of hCA II in complex with a benzoxaborole i... -

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Basic information

Entry
Database: PDB / ID: 5lmd
TitleThe crystal structure of hCA II in complex with a benzoxaborole inhibitor
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Benzoxaborole / zinc enzyme / 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 / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 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
Chem-RC4 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsDe Simone, G. / Alterio, V. / Esposito, D. / Di Fiore, A.
CitationJournal: Chem.Commun.(Camb.) / Year: 2016
Title: Benzoxaborole as a new chemotype for carbonic anhydrase inhibition.
Authors: Alterio, V. / Cadoni, R. / Esposito, D. / Vullo, D. / Fiore, A.D. / Monti, S.M. / Caporale, A. / Ruvo, M. / Sechi, M. / Dumy, P. / Supuran, C.T. / Simone, G. / Winum, J.Y.
History
DepositionJul 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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)29,8723
Polymers29,4771
Non-polymers3952
Water4,161231
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.427, 41.493, 72.149
Angle α, β, γ (deg.)90.000, 104.400, 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: 29477.307 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 K-12 (bacteria) / 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-RC4 / 1-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-4-yl]-3-(2-methoxy-5-methyl-phenyl)urea


Mass: 329.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18BN2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 1.4 M Sodium Citrate 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 25797 / % possible obs: 95.4 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.081 / Net I/av σ(I): 21.396 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.7-1.7330.333170.9
1.73-1.763.50.325182.3
1.76-1.794.30.311194.4
1.79-1.835.10.274197.4
1.83-1.875.50.241198.8
1.87-1.9160.22199.6
1.91-1.966.60.193199.9
1.96-2.0270.171100
2.02-2.0780.1551100
2.07-2.148.50.1371100
2.14-2.228.50.1311100
2.22-2.318.50.1261100
2.31-2.418.60.1011100
2.41-2.548.60.0941100
2.54-2.78.70.0861100
2.7-2.918.60.0751100
2.91-3.28.70.0621100
3.2-3.667.80.056174.1
3.66-4.617.30.044191.5
4.61-508.20.036199

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Processing

Software
NameVersionClassification
d*TREKdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1CA2

1ca2


Resolution: 1.7→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 1208 4.5 %Random selection
Rwork0.1656 ---
obs-24819 91.9 %-
Solvent computationBsol: 44.9861 Å2
Displacement parametersBiso max: 45.57 Å2 / Biso mean: 14.0393 Å2 / Biso min: 3.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.192 Å2
2---0.451 Å2-0 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 25 231 2305
Biso mean--19.83 23.37 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_d1.649
X-RAY DIFFRACTIONc_mcbond_it1.2331.5
X-RAY DIFFRACTIONc_scbond_it2.0842
X-RAY DIFFRACTIONc_mcangle_it1.8172
X-RAY DIFFRACTIONc_scangle_it3.0612.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.760.239910.21291762185369.5
1.76-1.830.24551230.20432262238589.4
1.83-1.910.24581220.18542382250493
1.91-2.020.19831080.15762447255595.5
2.02-2.140.20621370.15312492262997.7
2.14-2.310.19151140.17392473258795.6
2.31-2.540.2071130.17162515262898.1
2.54-2.910.21151490.17232534268398.9
2.91-3.660.19771280.15972218234686.1
3.66-500.16491230.14542526264994.6

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