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- PDB-5ehe: Crystal structure of human carbonic anhydrase isozyme II with 3-(... -

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Basic information

Entry
Database: PDB / ID: 5ehe
TitleCrystal structure of human carbonic anhydrase isozyme II with 3-(benzylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex
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 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
DI(HYDROXYETHYL)ETHER / Chem-WWO / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: ChemMedChem / Year: 2017
Title: Intrinsic Thermodynamics and Structures of 2,4- and 3,4-Substituted Fluorinated Benzenesulfonamides Binding to Carbonic Anhydrases.
Authors: Zubriene, A. / Smirnov, A. / Dudutiene, V. / Timm, D.D. / Matuliene, J. / Michailoviene, V. / Zaksauskas, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionOct 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 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)30,2377
Polymers29,2891
Non-polymers9476
Water3,927218
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint16 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.200, 41.026, 71.950
Angle α, β, γ (deg.)90.000, 104.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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 / Fragment: human carbonic anhydrase II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 6 types, 224 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Fragment: 3-(benzylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Fragment: Zn / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Fragment: BICINE / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Fragment: DIMETHYL SULFOXIDE / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-WWO / 3-(benzylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide


Mass: 424.415 Da / Num. of mol.: 1 / Fragment: N-(EHTYLSULFITE)MORPHOLINE / Source method: obtained synthetically / Formula: C15H15F3N2O5S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.01 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystallization buffer contains 0.1M sodium bicine (pH 9) and 2.6M sodium malonate (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.405→20.511 Å / Num. all: 37863 / Num. obs: 37863 / % possible obs: 98.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 14.855 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.036 / Rrim(I) all: 0.082 / Rsym value: 0.067 / Net I/av σ(I): 7.227 / Net I/σ(I): 20.2 / Num. measured all: 198008
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.5-1.585.30.3010.2472.72895554600.130.30.24714.397.7
1.58-1.685.30.2280.1893.52732451730.10.230.1896.498.1
1.68-1.795.30.1710.1414.82573548630.070.170.1419.798.3
1.79-1.945.30.1310.1086.22410345600.060.130.10815.698.6
1.94-2.125.30.1040.0837.92221442220.040.10.08322.898.9
2.12-2.375.30.0880.079.32015038260.040.090.072999.1
2.37-2.745.30.0750.0610.81787033970.030.080.0633.199.3
2.74-3.355.20.0640.05111.81499628800.030.060.05139.599.5
3.35-4.7450.0580.047131122922570.030.060.04745.499.3
4.74-20.514.40.060.04913543212250.030.060.04942.995.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.6.0117refinement
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLJ

3hlj


Resolution: 1.5→19.89 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.871 / SU R Cruickshank DPI: 0.088 / SU Rfree: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3808 10.1 %RANDOM
Rwork0.18 34042 --
obs0.183 37850 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.54 Å2 / Biso mean: 16.823 Å2 / Biso min: 5.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20.05 Å2
2---0.87 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 51 218 2318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022250
X-RAY DIFFRACTIONr_angle_refined_deg2.3021.9663071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7095279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39424.804102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81315359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.745157
X-RAY DIFFRACTIONr_chiral_restr0.1730.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211760
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 269 -
Rwork0.283 2486 -
all-2755 -
obs--97.38 %

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