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- PDB-5e2r: The crystal structure of the human carbonic anhydrase II in compl... -

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Basic information

Entry
Database: PDB / ID: 5e2r
TitleThe crystal structure of the human carbonic anhydrase II in complex with a 1,1'-biphenyl-4-sulfonamide inhibitor
ComponentsCarbonic anhydrase 2
KeywordsLYASE / 1'-BIPHENYL-4-SULFONAMIDE / COMPLEX / INHIBITOR
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 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'-(4-aminobenzoyl)biphenyl-4-sulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsAlterio, V. / De Simone, G.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Discovery of 1,1'-Biphenyl-4-sulfonamides as a New Class of Potent and Selective Carbonic Anhydrase XIV Inhibitors.
Authors: La Regina, G. / Coluccia, A. / Famiglini, V. / Pelliccia, S. / Monti, L. / Vullo, D. / Nuti, E. / Alterio, V. / De Simone, G. / Monti, S.M. / Pan, P. / Parkkila, S. / Supuran, C.T. / Rossello, A. / Silvestri, R.
History
DepositionOct 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Jan 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

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9874
Polymers29,4771
Non-polymers5103
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-7 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.229, 41.340, 71.804
Angle α, β, γ (deg.)90.000, 104.270, 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: 29477.307 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-Gold(DE3)pLysS AG' (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-520 / 4'-(4-aminobenzoyl)biphenyl-4-sulfonamide


Mass: 352.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16N2O3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 40.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: Na-Citrate, Tris-HCl / PH range: 8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 30330 / % possible obs: 95 % / Redundancy: 4.2 % / Rsym value: 0.052 / Net I/σ(I): 23.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 5.8 / % possible all: 75.3

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Processing

Software
NameVersionClassification
CNSrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
CrystalCleardata collection
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1CA2

1ca2


Resolution: 1.6→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1478 4.6 %Random selection
Rwork0.172 28276 --
obs-29754 93.1 %-
Solvent computationBsol: 38.2567 Å2
Displacement parametersBiso max: 42.91 Å2 / Biso mean: 15.6 Å2 / Biso min: 4.58 Å2
Baniso -1Baniso -2Baniso -3
1--2.157 Å20 Å2-1.224 Å2
2--2.257 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 32 267 2375
Biso mean--18.92 24.14 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.457
X-RAY DIFFRACTIONc_mcbond_it1.1491.5
X-RAY DIFFRACTIONc_scbond_it1.9672
X-RAY DIFFRACTIONc_mcangle_it1.722
X-RAY DIFFRACTIONc_scangle_it2.8852.5

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