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- PDB-6h2z: The crystal structure of human carbonic anhydrase II in complex w... -

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Basic information

Entry
Database: PDB / ID: 6h2z
TitleThe crystal structure of human carbonic anhydrase II in complex with 4-(4-phenylpiperidine-1-carbonyl)benzenesulfonamide.
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Protein-inhibitor binding
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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / 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 / cytoplasm / cytosol
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-FKE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.94 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. ...Buemi, 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.
History
DepositionJul 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0715
Polymers29,4771
Non-polymers5944
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-7 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.350, 41.110, 71.670
Angle α, β, γ (deg.)90.00, 104.22, 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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FKE / 4-(4-phenylpiperidin-1-yl)carbonylbenzenesulfonamide


Mass: 344.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C18H20N2O3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.05 Å3/Da / Density % sol: 40.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: sodium citrate 1.3M, 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: Jan 29, 2018 / 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: 1.94→34.7 Å / Num. obs: 17564 / % possible obs: 98.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.063 / Rrim(I) all: 0.131 / Net I/σ(I): 11.5
Reflection shellResolution: 1.94→2.01 Å / Rmerge(I) obs: 0.418 / Num. unique obs: 1610 / Rpim(I) all: 0.336 / Rrim(I) all: 0.57 / % possible all: 90.2

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1CA2

1ca2


Resolution: 1.94→34.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.214 925 -
Rwork0.179 --
obs0.181 15722 92.8 %
Refinement stepCycle: LAST / Resolution: 1.94→34.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 37 158 2234
LS refinement shellResolution: 1.94→2.01 Å
RfactorNum. reflection% reflection
Rfree0.234 76 6.2 %
Rwork0.244 --
obs-1219 -

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