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- PDB-6wq7: Carbonic Anhydrase II Complexed with 2-((3-Aminopropyl)(phenethyl... -

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Basic information

Entry
Database: PDB / ID: 6wq7
TitleCarbonic Anhydrase II Complexed with 2-((3-Aminopropyl)(phenethyl)amino)-N-(4-fluorobenzyl)-N-(4-sulfamoylphenethyl)acetamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / Inhibitor / Sulfonamide / CAII / CA II / LYASE / LYASE-LYASE INHIBITOR complex
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, 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
Similarity search - Domain/homology
Chem-U6V / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.304 Å
AuthorsAndring, J.T. / Combs, J.E. / Lomelino, C. / McKenna, R.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Sulfonamide Inhibitors of Human Carbonic Anhydrases Designed through a Three-Tails Approach: Improving Ligand/Isoform Matching and Selectivity of Action.
Authors: Bonardi, A. / Nocentini, A. / Bua, S. / Combs, J. / Lomelino, C. / Andring, J. / Lucarini, L. / Sgambellone, S. / Masini, E. / McKenna, R. / Gratteri, P. / Supuran, C.T.
History
DepositionApr 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Oct 18, 2023Group: 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)30,0034
Polymers29,2891
Non-polymers7143
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.134, 41.302, 72.102
Angle α, β, γ (deg.)90.000, 104.330, 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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-U6V / N~2~-(3-aminopropyl)-N-[(4-fluorophenyl)methyl]-N~2~-(2-phenylethyl)-N-[2-(4-sulfamoylphenyl)ethyl]glycinamide


Mass: 526.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H35FN4O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M sodium citrate and 50mM Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.3→31.97 Å / Num. obs: 57221 / % possible obs: 97.5 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.026 / Rrim(I) all: 0.047 / Net I/σ(I): 15.6 / Num. measured all: 177367
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.331.70.437361621770.6740.3810.5831.775.9
7.14-31.973.20.02412183840.9980.0150.02841.198.3

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ks3

3ks3


Resolution: 1.304→25.28 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.69
RfactorNum. reflection% reflection
Rfree0.1813 2882 5.04 %
Rwork0.1597 --
obs0.1608 57194 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.42 Å2 / Biso mean: 19.0922 Å2 / Biso min: 7.17 Å2
Refinement stepCycle: final / Resolution: 1.304→25.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 81 239 2369
Biso mean--30.82 24.48 -
Num. residues----257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3044-1.32580.3311080.2914197075
1.3258-1.34860.29511030.2548232288
1.3486-1.37320.24391390.2217245193
1.3732-1.39960.20821500.2135259799
1.3996-1.42810.22711500.19632613100
1.4281-1.45920.22091270.1852664100
1.4592-1.49310.20221340.18062610100
1.4931-1.53050.19711410.1767264199
1.5305-1.57180.18791350.1745262799
1.5718-1.61810.1831510.17042616100
1.6181-1.67030.18731420.16222639100
1.6703-1.730.17151500.1565262899
1.73-1.79920.17831330.16172644100
1.7992-1.88110.15071260.1561265499
1.8811-1.98020.18651430.1505263699
1.9802-2.10420.15521390.1533264999
2.1042-2.26660.17511450.14972621100
2.2666-2.49450.15751610.1537263999
2.4945-2.85510.20361350.1612677100
2.8551-3.59540.17741530.1566265499
3.5954-25.280.16311170.1345276099

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