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- PDB-7oyp: Carbonic anhydrase II in complex with Hit3-t1 (MH172) -

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Basic information

Entry
Database: PDB / ID: 7oyp
TitleCarbonic anhydrase II in complex with Hit3-t1 (MH172)
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-3I4 / 4-methylbenzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 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)29,8724
Polymers29,2891
Non-polymers5833
Water6,179343
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11710 Å2
Unit cell
Length a, b, c (Å)42.325, 41.347, 72.403
Angle α, β, γ (deg.)90.000, 104.570, 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-3I4 / (2S)-3-oxidanyl-2-[2-[(4-sulfamoylphenyl)methoxyamino]ethanoylamino]propanamide


Mass: 346.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N4O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-4J8 / 4-methylbenzenesulfonamide


Mass: 171.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 41.25 %
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 PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.05→40.96 Å / Num. obs: 101502 / % possible obs: 89.5 % / Redundancy: 3.445 % / Biso Wilson estimate: 12.952 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.049 / Χ2: 0.809 / Net I/σ(I): 14.44 / Num. measured all: 349672
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
1.05-1.112.2910.371.93212191831292630.7760.48250.6
1.11-1.192.9160.2243.84342017105148880.9310.27387
1.19-1.283.6820.176.025858016024159080.9710.19999.3
1.28-1.413.6630.1188.735358414717146290.9840.13899.4
1.41-1.573.6270.0813.264787113329132000.9930.09399
1.57-1.823.7940.05420.714438311753116970.9960.06399.5
1.82-2.223.7080.03829.9236654999598840.9980.04598.9
2.22-3.143.6290.03435.8327921778476930.9980.03998.8
3.14-40.963.6960.02741.2416039439543390.9990.03298.7

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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: 1.05→40.96 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.766 / SU ML: 0.017 / SU R Cruickshank DPI: 0.0235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1343 2031 2 %RANDOM
Rwork0.1175 ---
obs0.1178 99471 89.53 %-
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: 53.52 Å2 / Biso mean: 13.688 Å2 / Biso min: 6.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.31 Å2
2---0.46 Å2-0 Å2
3---0.71 Å2
Refinement stepCycle: final / Resolution: 1.05→40.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 35 372 2451
Biso mean--18.26 26.06 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132257
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172005
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.643089
X-RAY DIFFRACTIONr_angle_other_deg1.5141.5854699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0675284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80123.478115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08815365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.816157
X-RAY DIFFRACTIONr_chiral_restr0.10.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022567
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02466
X-RAY DIFFRACTIONr_rigid_bond_restr1.89734262
LS refinement shellResolution: 1.05→1.076 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.227 68 -
Rwork0.246 3317 -
obs--40.36 %

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