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- PDB-6h38: The crystal structure of human carbonic anhydrase VII in complex ... -

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Basic information

Entry
Database: PDB / ID: 6h38
TitleThe crystal structure of human carbonic anhydrase VII in complex with 4-[(4-fluorophenyl)methyl]-1-piperazinyl]benzenesulfonamide.
ComponentsCarbonic anhydrase 7
KeywordsLYASE / Protein-Inhibitor Binding
Function / homology
Function and homology information


positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase VII / 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. ...Carbonic anhydrase VII / 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-FKK / Carbonic anhydrase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsBuemi, M.R. / Di Fiore, A. / De Luca, L. / Ferro, S. / Mancuso, F. / Monti, S.M. / Buonanno, M. / Angeli, A. / Russo, E. / De Sarro, G. ...Buemi, M.R. / Di Fiore, A. / De Luca, L. / Ferro, S. / Mancuso, F. / Monti, S.M. / Buonanno, M. / Angeli, A. / Russo, E. / De Sarro, G. / Supuran, C.T. / De Simone, G. / Gitto, R.
CitationJournal: Eur J Med Chem / Year: 2018
Title: Exploring structural properties of potent human carbonic anhydrase inhibitors bearing a 4-(cycloalkylamino-1-carbonyl)benzenesulfonamide moiety.
Authors: Buemi, M.R. / Di Fiore, A. / De Luca, L. / Angeli, A. / Mancuso, F. / Ferro, S. / Monti, S.M. / Buonanno, M. / Russo, E. / De Sarro, G. / De Simone, G. / Supuran, C.T. / Gitto, R.
History
DepositionJul 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5535
Polymers30,9261
Non-polymers6274
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-5 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.100, 89.240, 44.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Carbonic anhydrase 7 / Carbonate dehydratase VII / Carbonic anhydrase VII / CA-VII


Mass: 30925.693 Da / Num. of mol.: 1 / Mutation: C183S, C217S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P43166, 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-FKK / 4-[4-[(4-fluorophenyl)methyl]piperazin-1-yl]carbonylbenzenesulfonamide


Mass: 377.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20FN3O3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% v/v Peg3350, 0.2 M Ammonium acetate, 0.1 M Tris-HCl pH 8.5

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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: Apr 30, 2018 / Details: Mirror
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→34 Å / Num. obs: 28527 / % possible obs: 96.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.021 / Rrim(I) all: 0.052 / Net I/σ(I): 27.3
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.6 / Rpim(I) all: 0.34 / Rrim(I) all: 0.663 / % possible all: 90.2

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6G4T

6g4t


Resolution: 1.7→34 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.245 --
Rwork0.193 --
obs-26198 92.5 %
Refinement stepCycle: LAST / Resolution: 1.7→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 39 144 2238

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