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- PDB-5wlr: Carbonic Anhydrase IX-mimic in complex with aryloxy-2-hydroxyprop... -

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Basic information

Entry
Database: PDB / ID: 5wlr
TitleCarbonic Anhydrase IX-mimic in complex with aryloxy-2-hydroxypropylammine sulfonamide
ComponentsCarbonic Anhydrase IX-mimic
KeywordsLYASE/INHIBITOR / carbonic anhydrase / beta adrenergic receptor / sulfonamide / aryloxy-2-hydroxypropylammine / 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 / 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 / morphogenesis of an epithelium / 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 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
Chem-86B / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsLomelino, C.L. / Andring, J.T. / McKenna, R.
CitationJournal: To Be Published
Title: Hybrids for multitargeted therapy Beta Adrenergic Receptor modulators CAIs
Authors: Nocentini, A. / Ceruso, M. / Bua, S. / Lomelino, C.L. / Andring, J.T. / McKenna, R. / Lanzi, C. / Masini, E. / Pecori, R. / Matucci, R. / Filippi, L. / Gratteri, P. / Carta, F. / Selleri, S. / Supuran, C.T.
History
DepositionJul 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rpim_I_all
Revision 1.2Oct 4, 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 IX-mimic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5795
Polymers28,8441
Non-polymers7344
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-9 kcal/mol
Surface area11830 Å2
Unit cell
Length a, b, c (Å)42.381, 41.734, 72.503
Angle α, β, γ (deg.)90.000, 103.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic Anhydrase IX-mimic / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 28844.465 Da / Num. of mol.: 1 / Fragment: UNP residues 4-260
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-86B / 4-{(2S)-2-hydroxy-3-[(propan-2-yl)amino]propoxy}benzene-1-sulfonamide / aryloxy-2-hydroxypropylammine sulfonamide


Mass: 288.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N2O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M sodium citrate 50mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.49→35.2 Å / Num. obs: 60130 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 13 Å2 / Rpim(I) all: 0.026 / Net I/σ(I): 26.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.49→35.2 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.28
RfactorNum. reflection% reflectionSelection details
Rfree0.1723 2853 4.74 %0.05
Rwork0.1519 ---
obs0.1529 60130 72.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.47 Å2 / Biso mean: 19.5808 Å2 / Biso min: 7.6 Å2
Refinement stepCycle: final / Resolution: 1.49→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 45 199 2286
Biso mean--30.4 29.44 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062196
X-RAY DIFFRACTIONf_angle_d0.972999
X-RAY DIFFRACTIONf_chiral_restr0.084311
X-RAY DIFFRACTIONf_plane_restr0.01390
X-RAY DIFFRACTIONf_dihedral_angle_d18.505803
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.462-1.48720.2089830.21321801188445
1.4872-1.51430.2271980.19391945204349
1.5143-1.54340.19281100.18411932204249
1.5434-1.57490.1906930.17551999209249
1.5749-1.60910.18961000.16871969206950
1.6091-1.64660.21351000.17691994209450
1.6466-1.68770.1759950.17282052214751
1.6877-1.73340.20521110.17442133224454
1.7334-1.78440.18211170.16232354247159
1.7844-1.8420.18541320.15382581271365
1.842-1.90780.17371430.15122871301472
1.9078-1.98420.16671610.14453068322978
1.9842-2.07450.17311760.14623412358886
2.0745-2.18380.20191810.15033710389194
2.1838-2.32060.16581980.15443923412198
2.3206-2.49980.19991880.15583843403197
2.4998-2.75120.18641910.16043908409998
2.7512-3.14910.15871910.15853962415399
3.1491-3.96670.15812010.14183878407998
3.9667-35.20.14811840.1353942412699
Refinement TLS params.Method: refined / Origin x: -9.3923 Å / Origin y: -1.5654 Å / Origin z: 16.1658 Å
111213212223313233
T0.0894 Å2-0.0012 Å20.0028 Å2-0.0848 Å20.0016 Å2--0.0886 Å2
L0.7466 °2-0.0571 °20.0856 °2-0.5225 °2-0.0426 °2--0.6136 °2
S-0.0005 Å °0.0019 Å °0.0322 Å °-0.0218 Å °0.0083 Å °-0.003 Å °0.0093 Å °0.0146 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allD1 - 150
4X-RAY DIFFRACTION1allD151 - 199
5X-RAY DIFFRACTION1allD201 - 205
6X-RAY DIFFRACTION1allD206 - 209
7X-RAY DIFFRACTION1allC1 - 2
8X-RAY DIFFRACTION1allE400

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