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- PDB-7jo1: Carbonic Anhydrase IX Mimic Complexed with N-(5-sulfamoyl-1,3,4-t... -

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Basic information

Entry
Database: PDB / ID: 7jo1
TitleCarbonic Anhydrase IX Mimic Complexed with N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)butyramide
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 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
N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)butanamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 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)29,8455
Polymers29,2011
Non-polymers6444
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.612, 40.896, 71.332
Angle α, β, γ (deg.)90.000, 103.910, 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: 29200.887 Da / Num. of mol.: 1 / Mutation: A65S, N67Q, E69T, I91L, F131V, K170E, L204A
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-VFJ / N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)butanamide


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.04 Å3/Da / Density % sol: 39.78 %
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: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.499→31.73 Å / Num. obs: 34359 / % possible obs: 91.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 13.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Net I/σ(I): 21.1
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
1.5-1.5260.5811039017190.9040.2520.6353.392.2
8.21-31.736.60.024160224110.010.02661.996.3

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Processing

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

3ks3


Resolution: 1.499→30.104 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 1724 5.03 %
Rwork0.1823 32568 -
obs0.1838 34292 91.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.88 Å2 / Biso mean: 16.5621 Å2 / Biso min: 6.43 Å2
Refinement stepCycle: final / Resolution: 1.499→30.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 41 150 2233
Biso mean--26.11 23.94 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072252
X-RAY DIFFRACTIONf_angle_d1.0293077
X-RAY DIFFRACTIONf_chiral_restr0.083317
X-RAY DIFFRACTIONf_plane_restr0.006405
X-RAY DIFFRACTIONf_dihedral_angle_d19.621826
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4994-1.54350.32691370.2933274992
1.5435-1.59340.26421380.2168279794
1.5934-1.65030.22031620.197274193
1.6503-1.71640.23651410.1854284295
1.7164-1.79450.20031230.1853283296
1.7945-1.88910.23811450.1954284096
1.8891-2.00740.22661360.1915283195
2.0074-2.16240.19491580.186289597
2.1624-2.37990.19291120.1807203069
2.3799-2.72410.19361440.1821249583
2.7241-3.43130.21211920.1787284498
3.4313-30.1040.20471360.1525267290
Refinement TLS params.Method: refined / Origin x: -9.1238 Å / Origin y: -1.1911 Å / Origin z: 16.0515 Å
111213212223313233
T-0.0177 Å20.0445 Å20.0114 Å2--0.0119 Å2-0.014 Å2--0.015 Å2
L0.0474 °2-0.0212 °20.0167 °2-0.0226 °2-0.0091 °2--0.0323 °2
S-0.0207 Å °-0.0291 Å °0.0129 Å °-0.0961 Å °0.0401 Å °0.0163 Å °-0.0089 Å °0.0179 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allC1 - 134
3X-RAY DIFFRACTION1allC135 - 156
4X-RAY DIFFRACTION1allB262
5X-RAY DIFFRACTION1allD1
6X-RAY DIFFRACTION1allD2
7X-RAY DIFFRACTION1allE1

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