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- PDB-5wg7: Human Carbonic Anhydrase II complexed with AceK -

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Basic information

Entry
Database: PDB / ID: 5wg7
TitleHuman Carbonic Anhydrase II complexed with AceK
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase / acesulfame / 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 / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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 / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
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
Acesulfame / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsMurray, A.B. / Lomelino, C.L. / Supuran, C.T. / McKenna, R.
CitationJournal: J. Med. Chem. / Year: 2018
Title: "Seriously Sweet": Acesulfame K Exhibits Selective Inhibition Using Alternative Binding Modes in Carbonic Anhydrase Isoforms.
Authors: Murray, A.B. / Lomelino, C.L. / Supuran, C.T. / McKenna, R.
History
DepositionJul 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)30,25311
Polymers28,9331
Non-polymers1,32110
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: An SX.18MV-R Applied Photophysics stopped-flow instrument has been used to assay the catalytic/inhibition of various CA isozymes
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-7 kcal/mol
Surface area11640 Å2
Unit cell
Length a, b, c (Å)42.312, 41.067, 72.152
Angle α, β, γ (deg.)90.00, 103.84, 90.00
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: 28932.641 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-AUD / Acesulfame / 6-methyl-2H-1,2lambda~6~,3-oxathiazine-2,2,4(3H)-trione / Acesulfame potassium


Mass: 163.152 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H5NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 41.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 1.6 M sodium citrate and 50 mM Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9782 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.45→41.1 Å / Num. obs: 63242 / % possible obs: 96.7 % / Redundancy: 2.9 % / Net I/σ(I): 12.9

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Processing

Software
NameVersionClassification
PHENIX1.10pre_2097refinement
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 1.45→41.083 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.08
RfactorNum. reflection% reflection
Rfree0.1761 3024 4.78 %
Rwork0.1418 --
obs0.1434 63242 75.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→41.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 79 161 2289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052254
X-RAY DIFFRACTIONf_angle_d0.8583073
X-RAY DIFFRACTIONf_dihedral_angle_d14.161843
X-RAY DIFFRACTIONf_chiral_restr0.08308
X-RAY DIFFRACTIONf_plane_restr0.005395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4485-1.47120.185830.12791683X-RAY DIFFRACTION46
1.4712-1.49530.1851990.12871812X-RAY DIFFRACTION50
1.4953-1.52110.2061840.13061839X-RAY DIFFRACTION50
1.5211-1.54870.1916930.13551873X-RAY DIFFRACTION52
1.5487-1.57850.15521050.13111926X-RAY DIFFRACTION53
1.5785-1.61070.1783960.12382050X-RAY DIFFRACTION57
1.6107-1.64570.19591050.12112228X-RAY DIFFRACTION60
1.6457-1.6840.18381260.11672347X-RAY DIFFRACTION66
1.684-1.72610.1811140.11472634X-RAY DIFFRACTION72
1.7261-1.77280.1661510.11942868X-RAY DIFFRACTION79
1.7728-1.8250.17981500.12192905X-RAY DIFFRACTION82
1.825-1.88390.17081430.12373090X-RAY DIFFRACTION83
1.8839-1.95120.19081480.12682985X-RAY DIFFRACTION82
1.9512-2.02930.16641620.12483124X-RAY DIFFRACTION86
2.0293-2.12170.16941530.13143165X-RAY DIFFRACTION87
2.1217-2.23360.16741680.13543209X-RAY DIFFRACTION89
2.2336-2.37350.1691810.14173318X-RAY DIFFRACTION92
2.3735-2.55670.17981670.15263296X-RAY DIFFRACTION91
2.5567-2.8140.16611790.15913455X-RAY DIFFRACTION96
2.814-3.2210.18261730.16513511X-RAY DIFFRACTION97
3.221-4.05760.18611690.1443424X-RAY DIFFRACTION94
4.0576-41.09960.1721750.1533476X-RAY DIFFRACTION96

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