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- PDB-5sz4: Carbonic anhydrase IX-mimic in complex with 4-(phenyl)-benzenesul... -

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Basic information

Entry
Database: PDB / ID: 5sz4
TitleCarbonic anhydrase IX-mimic in complex with 4-(phenyl)-benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLyase/Lyase Inhibitor / sulfonamide / inhibitor / zinc-binding / 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 / 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
4-(phenyl)-benzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBhatt, A. / Mahon, B.P. / Cornelio, B. / McKenna, R.
CitationJournal: Chembiochem / Year: 2017
Title: Structure-Activity Relationships of Benzenesulfonamide-Based Inhibitors towards Carbonic Anhydrase Isoform Specificity.
Authors: Bhatt, A. / Mahon, B.P. / Cruzeiro, V.W. / Cornelio, B. / Laronze-Cochard, M. / Ceruso, M. / Sapi, J. / Rance, G.A. / Khlobystov, A.N. / Fontana, A. / Roitberg, A. / Supuran, C.T. / McKenna, R.
History
DepositionAug 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Oct 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2995
Polymers28,8441
Non-polymers4554
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.930, 41.294, 72.504
Angle α, β, γ (deg.)90.00, 103.61, 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: 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-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-72D / 4-(phenyl)-benzenesulfonamide / [1,1'-biphenyl]-4-sulfonamide


Mass: 233.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11NO2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.12 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 1.6M Sodium Citrate, 50mM Tris pH 7.8 / PH range: 7.2-8.2

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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: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→19.962 Å / Num. obs: 27269 / % possible obs: 98.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 14.47 Å2 / Rmerge(I) obs: 0.112 / Net I/av σ(I): 11.992 / Net I/σ(I): 3.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.69-1.7260.6180.877199.5
1.72-1.756.30.6140.498199.3
1.75-1.786.50.5410.815199
1.78-1.826.50.5370.513199.7
1.82-1.866.50.3990.918199.3
1.86-1.96.40.420.793199.8
1.9-1.956.50.360.64199.4
1.95-26.40.3270.861199
2-2.066.50.2690.886198.7
2.06-2.136.50.2280.976198.2
2.13-2.26.40.2390.915197.4
2.2-2.296.40.2170.972196.9
2.29-2.46.50.1940.978197.5
2.4-2.526.50.1310.984196.4
2.52-2.686.50.1440.984196.9
2.68-2.896.60.1450.966199
2.89-3.186.90.0830.9741100
3.18-3.637.20.0530.998199.8
3.63-4.577.30.050.997199.6
4.57-2070.0710.9961100

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Processing

Software
NameVersionClassification
PHENIX1.10pre_2097refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ks3

3ks3


Resolution: 1.6→19.962 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 1356 4.97 %
Rwork0.1831 --
obs0.1848 27269 84.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→19.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 25 180 2247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082147
X-RAY DIFFRACTIONf_angle_d1.2122916
X-RAY DIFFRACTIONf_dihedral_angle_d9.3532188
X-RAY DIFFRACTIONf_chiral_restr0.065306
X-RAY DIFFRACTIONf_plane_restr0.011375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5998-1.65690.3363580.23861069X-RAY DIFFRACTION35
1.6569-1.72320.274930.23771758X-RAY DIFFRACTION58
1.7232-1.80160.27751180.22032230X-RAY DIFFRACTION74
1.8016-1.89650.25821440.2122749X-RAY DIFFRACTION90
1.8965-2.01530.2381470.1962923X-RAY DIFFRACTION97
2.0153-2.17070.24941540.18633004X-RAY DIFFRACTION99
2.1707-2.38880.23091600.1882970X-RAY DIFFRACTION98
2.3888-2.73370.24121530.19183030X-RAY DIFFRACTION99
2.7337-3.44130.20681650.18563061X-RAY DIFFRACTION99
3.4413-19.9640.16491640.15163119X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.7782 Å / Origin y: 0.0905 Å / Origin z: 16.1401 Å
111213212223313233
T-0.0029 Å20.0216 Å20.0199 Å2--0.0255 Å2-0.0581 Å2---0.0318 Å2
L0.0234 °2-0.0005 °20.0142 °2-0.0202 °20.003 °2--0.0203 °2
S-0.0194 Å °-0.0089 Å °0.0646 Å °-0.0543 Å °0.0033 Å °0.0134 Å °0.0365 Å °0.0254 Å °0 Å °
Refinement TLS groupSelection details: all

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