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- PDB-6h3q: Crystal structure of human carbonic anhydrase II in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6h3q
TitleCrystal structure of human carbonic anhydrase II in complex with the 4-(5-(chloromethyl)-1,3-selenazol-2-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
Chem-FMH / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.31 Å
AuthorsFerraroni, M. / Angeli, A. / Supuran, C.
CitationJournal: Eur.J.Med.Chem. / Year: 2018
Title: Discovery of new 2, 5-disubstituted 1,3-selenazoles as selective human carbonic anhydrase IX inhibitors with potent anti-tumor activity.
Authors: Angeli, A. / Trallori, E. / Ferraroni, M. / Di Cesare Mannelli, L. / Ghelardini, C. / Supuran, C.T.
History
DepositionJul 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: 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)29,6903
Polymers29,2891
Non-polymers4012
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.378, 41.361, 72.047
Angle α, β, γ (deg.)90.000, 104.260, 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 BL21 (bacteria) / 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-FMH / 4-[5-(chloromethyl)-1,3-selenazol-2-yl]benzenesulfonamide


Mass: 335.669 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9ClN2O2SSe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
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: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.31→69.83 Å / Num. obs: 58339 / % possible obs: 99.9 % / Redundancy: 5.371 % / Biso Wilson estimate: 18.061 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.157 / Χ2: 0.964 / Net I/σ(I): 5.97 / Num. measured all: 313339
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.31-1.45.3351.0070.95104480.5031.116100
1.4-1.515.4280.7441.5696920.6850.82399.9
1.51-1.655.420.5142.6188440.830.5799.9
1.65-1.855.3290.3314.2484880.9240.36799.8
1.85-2.135.3450.1877.6771030.9730.207100
2.13-2.615.4120.12711.3662230.9860.14199.9
2.61-3.685.2550.0816.3548050.9940.08999.9
3.68-69.835.460.06222.0627360.9960.06999.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4FIK

4fik


Resolution: 1.31→69.83 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.358 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0545 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.056
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 2824 4.8 %RANDOM
Rwork0.1821 ---
obs0.1833 55460 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 186.31 Å2 / Biso mean: 16.73 Å2 / Biso min: 8.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å2-0.23 Å2
2--0.37 Å20 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 1.31→69.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 18 254 2321
Biso mean--26.71 27.75 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192138
X-RAY DIFFRACTIONr_bond_other_d0.0010.021938
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9562902
X-RAY DIFFRACTIONr_angle_other_deg0.88334529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg75259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69924.69498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52115357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.779157
X-RAY DIFFRACTIONr_chiral_restr0.1090.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
LS refinement shellResolution: 1.31→1.344 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 216 -
Rwork0.319 4047 -
all-4263 -
obs--99.42 %

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