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- PDB-5sz1: Carbonic anhydrase II in complex with 4-(2-methylphenyl)-benzenes... -

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Basic information

Entry
Database: PDB / ID: 5sz1
TitleCarbonic anhydrase II in complex with 4-(2-methylphenyl)-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 / 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 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-(2-methylphenyl)-benzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6648
Polymers28,9331
Non-polymers7317
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.215, 41.284, 71.873
Angle α, β, γ (deg.)90.000, 104.200, 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: 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

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Non-polymers , 5 types, 244 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-72E / 4-(2-methylphenyl)-benzenesulfonamide / 2'-methyl[1,1'-biphenyl]-4-sulfonamide


Mass: 247.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13NO2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 41.39 %
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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. obs: 33928 / % possible obs: 96.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 15.55 Å2 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.025 / Rrim(I) all: 0.051 / Χ2: 0.875 / Net I/av σ(I): 27.323 / Net I/σ(I): 13.4 / Num. measured all: 131481
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.55-1.583.60.5630.828194.5
1.58-1.613.90.4710.865196.4
1.61-1.6440.4130.894196.2
1.64-1.6740.3630.9196.8
1.67-1.7140.2820.934196.8
1.71-1.7540.2270.953197.1
1.75-1.793.90.1890.967196.7
1.79-1.843.90.1520.976196.7
1.84-1.893.90.1220.984196.5
1.89-1.953.80.0990.989195.8
1.95-2.023.90.0830.991194.4
2.02-2.13.70.0670.995194.1
2.1-2.23.70.0570.995193.8
2.2-2.313.60.0490.996193.1
2.31-2.463.50.0430.996193.8
2.46-2.653.50.0370.997195
2.65-2.913.60.0330.997199.2
2.91-3.3340.0320.997199.9
3.33-4.24.40.0350.997199.7
4.2-204.30.0370.998199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXdev_1839refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ks3

3ks3


Resolution: 1.55→19.915 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.98
RfactorNum. reflection% reflection
Rfree0.1854 1678 5 %
Rwork0.1568 --
obs0.1583 33540 94.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.15 Å2 / Biso mean: 18.9588 Å2 / Biso min: 7.55 Å2
Refinement stepCycle: final / Resolution: 1.55→19.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 42 239 2330
Biso mean--26.76 29.23 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072179
X-RAY DIFFRACTIONf_angle_d1.1312955
X-RAY DIFFRACTIONf_chiral_restr0.047309
X-RAY DIFFRACTIONf_plane_restr0.006378
X-RAY DIFFRACTIONf_dihedral_angle_d13.624794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5467-1.59220.30541150.27142251236681
1.5922-1.64360.23841450.21272610275595
1.6436-1.70230.22431370.18522691282897
1.7023-1.77040.20551380.18582699283797
1.7704-1.85090.20911420.16212682282497
1.8509-1.94850.21390.14522659279896
1.9485-2.07040.18291430.14362649279295
2.0704-2.23010.16621310.14872603273493
2.2301-2.45410.18691400.15092619275994
2.4541-2.80840.18491460.16132714286097
2.8084-3.53510.19821470.15128112958100
3.5351-19.91670.15071550.144728743029100
Refinement TLS params.Method: refined / Origin x: -5.9834 Å / Origin y: -0.6202 Å / Origin z: 85.6494 Å
111213212223313233
T0.0933 Å2-0.0026 Å20.0007 Å2-0.0901 Å20.0001 Å2--0.0943 Å2
L0.5336 °2-0.0883 °20.0299 °2-0.4389 °2-0.0017 °2--0.4855 °2
S-0.0021 Å °-0.0274 Å °0.0101 Å °-0.0324 Å °0.0046 Å °0.0047 Å °0.0039 Å °0.0128 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD2 - 252
4X-RAY DIFFRACTION1allC400
5X-RAY DIFFRACTION1allC401
6X-RAY DIFFRACTION1allE1 - 2
7X-RAY DIFFRACTION1allE3
8X-RAY DIFFRACTION1allF1

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