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

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Basic information

Entry
Database: PDB / ID: 4yxi
TitleHuman Carbonic Anhydrase II complexed with an inhibitor with a benzenesulfonamide group (2).
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Protein-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 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
4-methylbenzenesulfonamide / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 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 23, 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)30,1116
Polymers29,2891
Non-polymers8225
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-12 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.463, 41.529, 72.453
Angle α, β, γ (deg.)90.00, 104.48, 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, 263 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-4J8 / 4-methylbenzenesulfonamide


Mass: 171.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9NO2S
#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.: 258 / 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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 293 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: 0.96→50 Å / Num. obs: 148298 / % possible obs: 99.2 % / Redundancy: 3.18 % / Biso Wilson estimate: 8 Å2 / Rsym value: 0.044 / Net I/σ(I): 13.25
Reflection shellResolution: 0.96→1.02 Å / Redundancy: 3.18 % / Mean I/σ(I) obs: 2.37 / % possible all: 98.1

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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: 0.96→40.116 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 12.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1533 7415 5 %Random selection
Rwork0.1404 ---
obs0.1411 148294 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.96→40.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 39 258 2318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052265
X-RAY DIFFRACTIONf_angle_d1.1113101
X-RAY DIFFRACTIONf_dihedral_angle_d12.02838
X-RAY DIFFRACTIONf_chiral_restr0.081318
X-RAY DIFFRACTIONf_plane_restr0.005428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9591-0.970.2412240.21694257X-RAY DIFFRACTION91
0.97-0.98140.22562470.19694704X-RAY DIFFRACTION100
0.9814-0.99340.21282500.18834751X-RAY DIFFRACTION100
0.9934-1.00590.1892480.18074707X-RAY DIFFRACTION100
1.0059-1.01920.19042450.17654660X-RAY DIFFRACTION100
1.0192-1.03310.18142480.16284697X-RAY DIFFRACTION99
1.0331-1.04790.17442470.16044694X-RAY DIFFRACTION100
1.0479-1.06350.16332510.14794771X-RAY DIFFRACTION100
1.0635-1.08020.15672450.13744657X-RAY DIFFRACTION100
1.0802-1.09790.14932480.12844709X-RAY DIFFRACTION100
1.0979-1.11680.15492480.1264724X-RAY DIFFRACTION100
1.1168-1.13710.13652460.11924665X-RAY DIFFRACTION100
1.1371-1.1590.13022490.11834730X-RAY DIFFRACTION100
1.159-1.18260.13682480.1174723X-RAY DIFFRACTION100
1.1826-1.20840.12812470.11754688X-RAY DIFFRACTION100
1.2084-1.23650.12962470.11744695X-RAY DIFFRACTION100
1.2365-1.26740.13892490.11834729X-RAY DIFFRACTION100
1.2674-1.30170.11532490.11584729X-RAY DIFFRACTION100
1.3017-1.340.13342470.11944703X-RAY DIFFRACTION100
1.34-1.38320.13052490.12154722X-RAY DIFFRACTION100
1.3832-1.43270.13632480.13044706X-RAY DIFFRACTION100
1.4327-1.490.12842470.12464702X-RAY DIFFRACTION100
1.49-1.55780.14842470.12834682X-RAY DIFFRACTION99
1.5578-1.640.14472480.12974718X-RAY DIFFRACTION99
1.64-1.74270.13412450.13844663X-RAY DIFFRACTION99
1.7427-1.87730.16012470.14474685X-RAY DIFFRACTION99
1.8773-2.06620.15412490.1484740X-RAY DIFFRACTION99
2.0662-2.36520.1452480.14984711X-RAY DIFFRACTION99
2.3652-2.97970.17222490.15734733X-RAY DIFFRACTION99
2.9797-40.15080.16692550.1434824X-RAY DIFFRACTION99

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