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- PDB-7oyo: Carbonic anhydrase II in complex with Hit4 (MH70) -

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Basic information

Entry
Database: PDB / ID: 7oyo
TitleCarbonic anhydrase II in complex with Hit4 (MH70)
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase / 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
Chem-TKR / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.03 Å
AuthorsKugler, M. / Brynda, J. / Rezacova, P.
CitationJournal: Rsc Med Chem / Year: 2023
Title: Identification of specific carbonic anhydrase inhibitors via in situ click chemistry, phage-display and synthetic peptide libraries: comparison of the methods and structural study.
Authors: Kugler, M. / Hadzima, M. / Dzijak, R. / Rampmaier, R. / Srb, P. / Vrzal, L. / Voburka, Z. / Majer, P. / Rezacova, P. / Vrabel, M.
History
DepositionJun 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,8204
Polymers29,2891
Non-polymers5313
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint4 kcal/mol
Surface area11400 Å2
Unit cell
Length a, b, c (Å)42.245, 41.384, 72.236
Angle α, β, γ (deg.)90.000, 104.490, 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) / 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-TKR / [1-[2-oxidanylidene-2-[2-(4-sulfamoylphenyl)ethylamino]ethyl]-1,2,3-triazolidin-4-yl]methyl hydrogen carbonate


Mass: 387.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N5O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 41.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris-H2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.03→40.9 Å / Num. obs: 108711 / % possible obs: 90.8 % / Redundancy: 3.851 % / Biso Wilson estimate: 13.231 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.074 / Χ2: 1.01 / Net I/σ(I): 10.11 / Num. measured all: 418659
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.03-1.093.7210.6391.635404519250145230.7210.74475.4
1.09-1.173.8770.3633.086376318075164460.8920.42191
1.17-1.263.7560.2244.85783916907154010.9490.2691.1
1.26-1.384.0060.157.375895515554147160.9760.17394.6
1.38-1.543.8750.09910.645211914070134500.9870.11595.6
1.54-1.783.8140.06915.374414212434115730.9930.0893.1
1.78-2.183.9630.05420.964084510572103060.9950.06297.5
2.18-3.083.7050.04923.4128573820277120.9950.05794
3.08-40.94.0090.04927.3518378463045840.9950.05799

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3PO6

3po6


Resolution: 1.03→40.9 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.818 / SU ML: 0.018 / SU R Cruickshank DPI: 0.0251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.167 1088 1 %RANDOM
Rwork0.1362 ---
obs0.1365 107622 90.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 89.87 Å2 / Biso mean: 15.252 Å2 / Biso min: 8.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0.11 Å2
2---0.25 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: final / Resolution: 1.03→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 22 382 2426
Biso mean--25.89 28.19 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132228
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172005
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.6413047
X-RAY DIFFRACTIONr_angle_other_deg1.5411.5844697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1955284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08123.636110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.62715366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.753158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022532
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02460
X-RAY DIFFRACTIONr_rigid_bond_restr7.78734232
LS refinement shellResolution: 1.03→1.056 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.308 58 -
Rwork0.291 5677 -
obs--64.96 %

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