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- PDB-6wq4: Carbonic Anhydrase II Complexed with 2-((2-Cyanoethyl)(phenethyl)... -

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Basic information

Entry
Database: PDB / ID: 6wq4
TitleCarbonic Anhydrase II Complexed with 2-((2-Cyanoethyl)(phenethyl)amino)-N-phenethyl-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 / cyanamide hydratase activity / 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 / cyanamide hydratase activity / 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 / cytosol / cytoplasm
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-U7A / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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)30,0875
Polymers29,2891
Non-polymers7984
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.365, 41.515, 72.262
Angle α, β, γ (deg.)90.000, 104.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 213 molecules

#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-U7A / N~2~-(2-cyanoethyl)-N,N~2~-bis(2-phenylethyl)-N-[2-(4-sulfamoylphenyl)ethyl]glycinamide


Mass: 518.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H34N4O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M sodium citrate and 50mM Tris at pH 7.8

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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 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.3→34.89 Å / Num. obs: 57535 / % possible obs: 97.5 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.025 / Rrim(I) all: 0.047 / Net I/σ(I): 16 / Num. measured all: 179193
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
1.3-1.331.70.349371721640.8210.3050.4662.174.2
7.15-34.893.20.02712263890.9980.0170.03239.898.4

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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: 1.35→32.108 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.2
RfactorNum. reflection% reflection
Rfree0.1724 2696 5.13 %
Rwork0.1539 --
obs0.1548 52575 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.27 Å2 / Biso mean: 16.1773 Å2 / Biso min: 5.45 Å2
Refinement stepCycle: final / Resolution: 1.35→32.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 94 209 2352
Biso mean--17.79 21.93 -
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 (%)
1.35-1.37430.30241070.2435194573
1.3743-1.40070.21621470.2114239992
1.4007-1.42930.23091440.1905267999
1.4293-1.46040.24221450.18012637100
1.4604-1.49440.2161430.17382650100
1.4944-1.53170.1931600.172657100
1.5317-1.57320.19771320.16422693100
1.5732-1.61950.18481470.15852631100
1.6195-1.67170.17031150.15972695100
1.6717-1.73150.18651540.15952668100
1.7315-1.80080.18181650.15522664100
1.8008-1.88270.18751440.15032653100
1.8827-1.9820.17141400.14682695100
1.982-2.10610.15431310.14242678100
2.1061-2.26870.15991560.14352654100
2.2687-2.49690.14271380.14932719100
2.4969-2.85810.15921280.15852695100
2.8581-3.60010.15891500.15222702100
3.6001-32.1080.1631500.1366276599

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