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- PDB-5n25: Crystal structure of human carbonic anhydrase II in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5n25
TitleCrystal structure of human carbonic anhydrase II in complex with the inhibitor 4-Pyridin-3-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 / 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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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
4-pyridin-3-ylbenzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsFerraroni, M. / Supuran, C.T. / Scozzafava, A. / Carta, F.
CitationJournal: Inorg.Chim.Acta. / Year: 2018
Title: Sulfonamide carbonic anhydrase inhibitors: Zinc coordination and tail effects influence inhibitory efficacy and selectivity for different isoforms
Authors: Ferraroni, M. / Cornelio, B. / Sapi, J. / Supuran, C.T. / Scozzafava, A.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: 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

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9155
Polymers29,2891
Non-polymers6264
Water6,089338
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-7 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.389, 41.188, 71.794
Angle α, β, γ (deg.)90.000, 104.410, 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) / Strain (production host): BL21 / 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-8HK / 4-pyridin-3-ylbenzenesulfonamide


Mass: 234.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10N2O2S
#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.: 338 / 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: 40.65 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 8 / Details: 1.5 M sodium citrate, Tris 50 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979783 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979783 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 45430 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 3.081 % / Biso Wilson estimate: 17.827 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.095 / Χ2: 0.955 / Net I/σ(I): 10.76 / Num. measured all: 139982
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.493.1030.7121.6571310.5770.86294.1
1.49-1.593.1170.4432.6967940.7670.53794.8
1.59-1.723.1110.2784.1463810.8930.33795.5
1.72-1.883.1060.1577.159140.9630.1996.5
1.88-2.13.0890.08612.1953850.9880.10596.5
2.1-2.423.0610.05817.1847750.9930.07197.2
2.42-2.973.0180.04621.8640900.9960.05697.5
2.97-4.193.0150.03230.3731730.9980.03997.3
4.19-302.9640.03131.917860.9970.03895.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4FIK

4fik


Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.298 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0679 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 2256 5 %RANDOM
Rwork0.1722 ---
obs0.1735 43159 95.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.17 Å2 / Biso mean: 14.02 Å2 / Biso min: 6.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.05 Å2
2---0.19 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 39 338 2408
Biso mean--12.34 26.75 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192211
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9373024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57825102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52715363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.494157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211809
LS refinement shellResolution: 1.402→1.438 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 175 -
Rwork0.291 3096 -
all-3271 -
obs--94.46 %

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