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- PDB-6rg4: Crystal structure of human Carbonic anhydrase II in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6rg4
TitleCrystal structure of human Carbonic anhydrase II in complex with (R)-4-(2-benzyl-4-methylpiperazin-1-yl)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 / 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, 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-K45 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 Å
AuthorsFerraroni, M. / Angeli, A. / Supuran, C.
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 16, 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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)29,9125
Polymers29,2891
Non-polymers6234
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-7 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.370, 41.299, 71.936
Angle α, β, γ (deg.)90.000, 104.380, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K45 / 4-[(3~{S})-4-methyl-3-(phenylmethyl)piperazin-1-yl]carbonylbenzenesulfonamide


Mass: 373.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N3O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1.6 sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.827 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.25→41.08 Å / Num. obs: 66147 / % possible obs: 99.1 % / Redundancy: 3.332 % / Biso Wilson estimate: 21.135 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.069 / Χ2: 1.036 / Net I/σ(I): 9.39 / Num. measured all: 220412 / Scaling rejects: 4
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
1.25-1.333.2270.9920.793600211257111560.5411.18999.1
1.33-1.443.3960.5371.773931011707115770.8150.63798.9
1.44-1.583.1880.2613.793296510535103410.9370.31498.2
1.58-1.763.4460.1427.6331136912490350.9770.16899
1.76-2.043.3140.07813.228282855085350.9910.09399.8
2.04-2.493.5130.05419.9824370695469380.9950.06499.8
2.49-3.523.3070.04125.0118151552054880.9970.04999.4
3.52-41.083.3140.03230.910196310630770.9980.03899.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4FIK

4fik


Resolution: 1.25→41.08 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.349 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0485 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 3239 4.9 %RANDOM
Rwork0.1556 ---
obs0.1577 62531 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.44 Å2 / Biso mean: 18.175 Å2 / Biso min: 8.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0.31 Å2
2--0.21 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.25→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 39 279 2377
Biso mean--39.53 30.32 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132215
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172014
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.6383021
X-RAY DIFFRACTIONr_angle_other_deg1.5271.5994722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1635275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27523.853109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01815367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.003157
X-RAY DIFFRACTIONr_chiral_restr0.110.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_rigid_bond_restr3.70834229
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.564 235 -
Rwork0.619 4596 -
all-4831 -
obs--98.21 %

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