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- PDB-6h34: The crystal structure of human carbonic anhydrase II in complex w... -

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Basic information

Entry
Database: PDB / ID: 6h34
TitleThe crystal structure of human carbonic anhydrase II in complex with 4-[(4-fluorophenyl)methyl]-1-piperazinyl]benzenesulfonamide.
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Protein-inhibitor binding / benzenesulfonamide
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of anion transport / secretion / carbon dioxide transport / arylesterase activity / regulation of chloride transport / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of osteoclast differentiation ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of anion transport / secretion / carbon dioxide transport / arylesterase activity / regulation of chloride transport / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of osteoclast differentiation / positive regulation of synaptic transmission, GABAergic / response to pH / morphogenesis of an epithelium / cellular response to fluid shear stress / carbonic anhydrase / carbonate dehydratase activity / response to steroid hormone / response to zinc ion / odontogenesis of dentin-containing tooth / positive regulation of bone resorption / microvillus / bicarbonate transport / kidney development / apical part of cell / myelin sheath / basolateral plasma membrane / response to estrogen / axon / go:0005623: / zinc ion binding / extracellular exosome / plasma membrane / cytosol / cytoplasm
Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain superfamily / Carbonic anhydrase, alpha-class, conserved site / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase / Carbonic Anhydrase II / Roll / Alpha Beta
Carbonic anhydrase 2
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsBuemi, M.R. / Di Fiore, A. / De Luca, L. / Ferro, S. / Mancuso, F. / Monti, S.M. / Buonanno, M. / Angeli, A. / Russo, E. / De Sarro, G. / Supuran, C.T. / De Simone, G. / Gitto, R.
CitationJournal: Eur J Med Chem / Year: 2018
Title: Exploring structural properties of potent human carbonic anhydrase inhibitors bearing a 4-(cycloalkylamino-1-carbonyl)benzenesulfonamide moiety.
Authors: Buemi, M.R. / Di Fiore, A. / De Luca, L. / Angeli, A. / Mancuso, F. / Ferro, S. / Monti, S.M. / Buonanno, M. / Russo, E. / De Sarro, G. / De Simone, G. / Supuran, C.T. / Gitto, R.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release

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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)30,0124
Polymers29,4771
Non-polymers5353
Water4,125229
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-7 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)42.320, 41.340, 72.110
Angle α, β, γ (deg.)90.00, 104.34, 90.00
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 (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FKK / 4-[4-[(4-fluorophenyl)methyl]piperazin-1-yl]carbonylbenzenesulfonamide


Mass: 377.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20FN3O3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Sodium citrate 1.3 M, Tris-HCl 0.1 M pH 8.5

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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: Dec 19, 2017 / Details: MIRROR
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.55→29.1 Å / Num. obs: 33156 / % possible obs: 93.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.029 / Rrim(I) all: 0.063 / Net I/σ(I): 21.8
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 4.4 / Rpim(I) all: 0.18 / Rrim(I) all: 0.309 / % possible all: 82.5

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1CA2
Resolution: 1.55→29.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.206 --
Rwork0.171 --
Obs-31223 91.1 %
Refinement stepCycle: LAST / Resolution: 1.55→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 33 229 2311

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