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- PDB-4yyt: Human Carbonic Anhydrase II complexed with an inhibitor with a be... -

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Basic information

Entry
Database: PDB / ID: 4yyt
TitleHuman Carbonic Anhydrase II complexed with an inhibitor with a benzenesulfonamide group (5).
ComponentsCarbonic anhydrase 2
KeywordsLYASE
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 / 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
MERCURIBENZOIC ACID / 4-(2-hydroxyethyl)benzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsRechlin, C. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Union/ERC268145-DrugProfilBind
CitationJournal: J.Med.Chem. / Year: 2016
Title: Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies.
Authors: Gaspari, R. / Rechlin, C. / Heine, A. / Bottegoni, G. / Rocchia, W. / Schwarz, D. / Bomke, J. / Gerber, H.D. / Klebe, G. / Cavalli, A.
History
DepositionMar 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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)30,5738
Polymers29,2891
Non-polymers1,2847
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-12 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.463, 41.703, 72.321
Angle α, β, γ (deg.)90.00, 104.33, 90.00
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 / Plasmid: PGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CODON PLUS / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 252 molecules

#2: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-S2O / 4-(2-hydroxyethyl)benzenesulfonamide


Mass: 201.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H11NO3S
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.5 uL of the protein solution (10 mg/ml hCAII in 50 mM Tris pH 7.8) were mixed with 2.5 uL of the well solution (2.7 M (NH4)SO4, 100 mM Tris, pH 7.8, saturated with p- ...Details: 2.5 uL of the protein solution (10 mg/ml hCAII in 50 mM Tris pH 7.8) were mixed with 2.5 uL of the well solution (2.7 M (NH4)SO4, 100 mM Tris, pH 7.8, saturated with p-chloromercurybenzoicacid) and placed as a hanging drop. Crystals appeared after several days. The crystals were soaked in 3.0 M (NH4)SO4, 100 mM Tris, pH 7.8, saturated with the inhibitor, for 1 day.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.07→50 Å / Num. obs: 107591 / % possible obs: 99.3 % / Redundancy: 3.19 % / Biso Wilson estimate: 7.799 Å2 / Rsym value: 0.058 / Net I/σ(I): 11.6
Reflection shellResolution: 1.07→1.13 Å / Redundancy: 3.03 % / Mean I/σ(I) obs: 2.13 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1492)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CNI

1cni


Resolution: 1.07→41.142 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1658 5380 5 %
Rwork0.143 --
obs0.1441 107587 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.07→41.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 65 245 2326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052271
X-RAY DIFFRACTIONf_angle_d1.1093108
X-RAY DIFFRACTIONf_dihedral_angle_d11.801848
X-RAY DIFFRACTIONf_chiral_restr0.081318
X-RAY DIFFRACTIONf_plane_restr0.005443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0695-1.08160.23171740.23713300X-RAY DIFFRACTION97
1.0816-1.09440.24331770.2213376X-RAY DIFFRACTION99
1.0944-1.10770.2311760.21063344X-RAY DIFFRACTION99
1.1077-1.12170.21431820.20463454X-RAY DIFFRACTION100
1.1217-1.13650.21331760.18543350X-RAY DIFFRACTION100
1.1365-1.15210.19161810.1773439X-RAY DIFFRACTION99
1.1521-1.16850.16271780.16993368X-RAY DIFFRACTION99
1.1685-1.1860.1921800.16813415X-RAY DIFFRACTION100
1.186-1.20450.19461760.15713353X-RAY DIFFRACTION100
1.2045-1.22420.15191810.14973444X-RAY DIFFRACTION100
1.2242-1.24540.15761810.14823426X-RAY DIFFRACTION100
1.2454-1.2680.17491790.14673406X-RAY DIFFRACTION100
1.268-1.29240.15991780.13893377X-RAY DIFFRACTION100
1.2924-1.31880.15371790.12933418X-RAY DIFFRACTION100
1.3188-1.34750.14811800.13043410X-RAY DIFFRACTION100
1.3475-1.37880.14991790.12623402X-RAY DIFFRACTION99
1.3788-1.41330.1491800.12793426X-RAY DIFFRACTION100
1.4133-1.45150.15461780.12563384X-RAY DIFFRACTION100
1.4515-1.49420.14761810.11923425X-RAY DIFFRACTION100
1.4942-1.54240.14221800.11943423X-RAY DIFFRACTION100
1.5424-1.59760.13641790.12063403X-RAY DIFFRACTION100
1.5976-1.66150.14511800.12013414X-RAY DIFFRACTION100
1.6615-1.73720.16931790.12453411X-RAY DIFFRACTION99
1.7372-1.82870.15521790.12983400X-RAY DIFFRACTION99
1.8287-1.94330.1711800.12873417X-RAY DIFFRACTION99
1.9433-2.09340.15461790.13483406X-RAY DIFFRACTION99
2.0934-2.3040.15371810.13883440X-RAY DIFFRACTION99
2.304-2.63740.18641790.14873404X-RAY DIFFRACTION99
2.6374-3.32260.16121810.1483438X-RAY DIFFRACTION99
3.3226-41.17250.16561870.14223534X-RAY DIFFRACTION99

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