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- PDB-4yx4: Human Carbonic Anhydrase II complexed with an inhibitor with a be... -

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Basic information

Entry
Database: PDB / ID: 4yx4
TitleHuman Carbonic Anhydrase II complexed with an inhibitor with a benzenesulfonamide group (1).
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Protein-Ligand-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 / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 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
benzenesulfonamide / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 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 22, 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)29,9255
Polymers29,2891
Non-polymers6364
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-12 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.385, 41.508, 72.254
Angle α, β, γ (deg.)90.00, 104.43, 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, 253 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#4: Chemical ChemComp-FB2 / benzenesulfonamide


Mass: 157.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO2S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
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: Feb 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.01→50 Å / Num. obs: 126327 / % possible obs: 98.7 % / Redundancy: 3.2 % / Rsym value: 0.049 / Net I/σ(I): 10.96
Reflection shellResolution: 1.01→1.07 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.01 / % possible all: 96

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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: 1.01→34.987 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1703 6317 5 %random selection
Rwork0.1509 ---
obs0.1518 126325 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.01→34.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 27 249 2288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052214
X-RAY DIFFRACTIONf_angle_d1.083024
X-RAY DIFFRACTIONf_dihedral_angle_d12.23808
X-RAY DIFFRACTIONf_chiral_restr0.078313
X-RAY DIFFRACTIONf_plane_restr0.005407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0086-1.02010.28751880.26953560X-RAY DIFFRACTION88
1.0201-1.03210.2732060.25563930X-RAY DIFFRACTION98
1.0321-1.04470.26242080.24783942X-RAY DIFFRACTION98
1.0447-1.05790.22192090.22073978X-RAY DIFFRACTION98
1.0579-1.07180.21462080.21553939X-RAY DIFFRACTION98
1.0718-1.08650.23292090.19653972X-RAY DIFFRACTION98
1.0865-1.1020.22982070.1873949X-RAY DIFFRACTION98
1.102-1.11850.16742120.17464019X-RAY DIFFRACTION99
1.1185-1.13590.17642090.1663970X-RAY DIFFRACTION99
1.1359-1.15460.17762100.16523987X-RAY DIFFRACTION99
1.1546-1.17450.18112100.16383993X-RAY DIFFRACTION99
1.1745-1.19580.18452130.16144038X-RAY DIFFRACTION99
1.1958-1.21880.17372080.1593957X-RAY DIFFRACTION99
1.2188-1.24370.15352120.15114033X-RAY DIFFRACTION99
1.2437-1.27080.16762100.15193984X-RAY DIFFRACTION99
1.2708-1.30030.16582140.14714072X-RAY DIFFRACTION100
1.3003-1.33280.15382130.14564042X-RAY DIFFRACTION100
1.3328-1.36890.16652140.1494063X-RAY DIFFRACTION100
1.3689-1.40920.16352110.14524026X-RAY DIFFRACTION100
1.4092-1.45460.16332120.14274009X-RAY DIFFRACTION100
1.4546-1.50660.15732130.13914059X-RAY DIFFRACTION100
1.5066-1.5670.14052140.13484055X-RAY DIFFRACTION100
1.567-1.63830.15812130.13374056X-RAY DIFFRACTION100
1.6383-1.72460.14772130.13934047X-RAY DIFFRACTION100
1.7246-1.83270.15972110.13984014X-RAY DIFFRACTION99
1.8327-1.97420.16142130.14194039X-RAY DIFFRACTION99
1.9742-2.17280.18072120.14464034X-RAY DIFFRACTION99
2.1728-2.48720.17712140.14634071X-RAY DIFFRACTION99
2.4872-3.13320.1752140.15344067X-RAY DIFFRACTION99
3.1332-35.00830.1552170.13674103X-RAY DIFFRACTION98

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