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- PDB-7jnw: Carbonic Anhydrase II Complexed with N-(5-sulfamoyl-1,3,4-thiadia... -

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Basic information

Entry
Database: PDB / ID: 7jnw
TitleCarbonic Anhydrase II Complexed with N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)isobutyramide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/INHIBITOR / Carbonic Anhydrase / CA Inhibitor / Structure Guided Drug Design / Carbonic Anhydrase II / Carbonic Anhydrase IX / CAII / CAIX / Sulfonamide / 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 / one-carbon metabolic process / 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-VFM / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.292 Å
AuthorsAndring, J.T. / McKenna, R.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structural Basis of Nanomolar Inhibition of Tumor-Associated Carbonic Anhydrase IX: X-Ray Crystallographic and Inhibition Study of Lipophilic Inhibitors with Acetazolamide Backbone.
Authors: Andring, J.T. / Fouch, M. / Akocak, S. / Angeli, A. / Supuran, C.T. / Ilies, M.A. / McKenna, R.
History
DepositionAug 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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)30,0256
Polymers29,2891
Non-polymers7365
Water6,161342
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.111, 41.050, 71.748
Angle α, β, γ (deg.)90.000, 104.330, 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, 347 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-VFM / 2-methyl-N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)propanamide


Mass: 250.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N4O3S2 / 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: 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.: 342 / 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: 2.05 Å3/Da / Density % sol: 40.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M Sodium Citrate, 50mM Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.29→30.44 Å / Num. obs: 55919 / % possible obs: 93.8 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.025 / Rrim(I) all: 0.057 / Net I/σ(I): 18 / Num. measured all: 258293
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
1.29-1.311.60.297242015150.8120.2620.3972.551.1
7.08-30.444.70.02918253920.9980.0150.03344.898.6

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ks3

3ks3


Resolution: 1.292→30.437 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1518 2794 5 %
Rwork0.126 53110 -
obs0.1273 55904 93.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.72 Å2 / Biso mean: 15.0365 Å2 / Biso min: 4.55 Å2
Refinement stepCycle: final / Resolution: 1.292→30.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 55 342 2446
Biso mean--25.73 26.35 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012259
X-RAY DIFFRACTIONf_angle_d2.0173084
X-RAY DIFFRACTIONf_chiral_restr0.088312
X-RAY DIFFRACTIONf_plane_restr0.013407
X-RAY DIFFRACTIONf_dihedral_angle_d15.577835
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.292-1.31410.2005600.1897147251
1.3141-1.3380.2406860.1594195770
1.338-1.36370.2037980.1475223278
1.3637-1.39150.1821310.1368255391
1.3915-1.42180.17081510.1307276397
1.4218-1.45490.17161430.1245271897
1.4549-1.49130.15951430.1184276598
1.4913-1.53160.16811560.1166277298
1.5316-1.57660.15271650.108274898
1.5766-1.62750.15991450.1093280298
1.6275-1.68570.14171490.1132277598
1.6857-1.75320.15881650.1119277999
1.7532-1.8330.13531470.1186282299
1.833-1.92960.11951280.1146280199
1.9296-2.05050.15621630.11652843100
2.0505-2.20870.13481360.112280099
2.2087-2.43090.14751510.12062857100
2.4309-2.78250.13521680.13222841100
2.7825-3.50480.16221730.13282856100
3.5048-30.4370.14771360.14172954100

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