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

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Basic information

Entry
Database: PDB / ID: 6rhk
TitleThe crystal structure of human carbonic anhydrase II in complex with 4-(3-benzylimidazolidine-1-carbonyl)benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE
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, 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
Chem-K4B / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsFerraroni, M. / Angeli, A. / Supuran, C.T.
CitationJournal: Bioorg.Chem. / Year: 2019
Title: Sulfonamides incorporating piperazine bioisosteres as potent human carbonic anhydrase I, II, IV and IX inhibitors.
Authors: Chiaramonte, N. / Bua, S. / Angeli, A. / Ferraroni, M. / Picchioni, I. / Bartolucci, G. / Braconi, L. / Dei, S. / Teodori, E. / Supuran, C.T. / Romanelli, M.N.
History
DepositionApr 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8845
Polymers29,2891
Non-polymers5954
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-8 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.600, 41.630, 72.350
Angle α, β, γ (deg.)90.00, 104.54, 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: 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-K4B / 4-[3-(phenylmethyl)imidazolidin-1-yl]carbonylbenzenesulfonamide


Mass: 345.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N3O3S
#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.: 230 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1.6 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→70.03 Å / Num. obs: 44092 / % possible obs: 99.3 % / Redundancy: 2.9 % / Net I/σ(I): 10
Reflection shellResolution: 1.44→1.47 Å / Num. unique obs: 2184

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIK

4fik


Resolution: 1.44→70.03 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.981 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.061 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17514 2257 5.1 %RANDOM
Rwork0.15461 ---
obs0.15569 41791 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.325 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0 Å20.04 Å2
2--0.24 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.44→70.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 37 230 2316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132182
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171992
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.6582967
X-RAY DIFFRACTIONr_angle_other_deg1.4591.5974661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9785267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7323.832107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26315365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.387157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022421
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02444
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6021.1681040
X-RAY DIFFRACTIONr_mcbond_other1.5561.1621037
X-RAY DIFFRACTIONr_mcangle_it2.4181.751298
X-RAY DIFFRACTIONr_mcangle_other2.4241.7521299
X-RAY DIFFRACTIONr_scbond_it2.671.4571142
X-RAY DIFFRACTIONr_scbond_other2.6691.4581143
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0182.0671664
X-RAY DIFFRACTIONr_long_range_B_refined5.11814.7112416
X-RAY DIFFRACTIONr_long_range_B_other5.1214.7232417
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.443→1.48 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 144 -
Rwork0.186 3093 -
obs--98.99 %

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