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

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Basic information

Entry
Database: PDB / ID: 4yxo
TitleHuman Carbonic Anhydrase II complexed with an inhibitor with a benzenesulfonamide group (3).
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
4-ethylbenzenesulfonamide / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 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)30,1396
Polymers29,2891
Non-polymers8505
Water4,234235
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-11 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.379, 41.575, 72.338
Angle α, β, γ (deg.)90.00, 104.29, 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 (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 240 molecules

#2: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-4JC / 4-ethylbenzenesulfonamide


Mass: 185.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 40.75 %
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: 1.06→50 Å / Num. obs: 108590 / % possible obs: 98 % / Redundancy: 3.63 % / Biso Wilson estimate: 8.578 Å2 / Rsym value: 0.077 / Net I/σ(I): 9.07
Reflection shellResolution: 1.06→1.12 Å / Redundancy: 3.55 % / Mean I/σ(I) obs: 2.07 / % possible all: 96.3

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Processing

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

1cni


Resolution: 1.06→35.05 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 15.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.164 5428 5 %Random selection
Rwork0.1486 ---
obs0.1494 108577 98.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.06→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 41 235 2291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052195
X-RAY DIFFRACTIONf_angle_d1.1132997
X-RAY DIFFRACTIONf_dihedral_angle_d11.79802
X-RAY DIFFRACTIONf_chiral_restr0.079312
X-RAY DIFFRACTIONf_plane_restr0.005407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0596-1.07160.28061730.2543289X-RAY DIFFRACTION96
1.0716-1.08430.22371770.23733367X-RAY DIFFRACTION96
1.0843-1.09750.21741770.21793374X-RAY DIFFRACTION96
1.0975-1.11140.23191760.2093338X-RAY DIFFRACTION96
1.1114-1.1260.2111800.18593422X-RAY DIFFRACTION97
1.126-1.14140.21491760.1853341X-RAY DIFFRACTION97
1.1414-1.15770.20911750.1823335X-RAY DIFFRACTION97
1.1577-1.1750.18521780.18313375X-RAY DIFFRACTION96
1.175-1.19340.18581790.17963394X-RAY DIFFRACTION97
1.1934-1.21290.15451800.15283420X-RAY DIFFRACTION97
1.2129-1.23390.17391750.15143327X-RAY DIFFRACTION96
1.2339-1.25630.18021800.14823430X-RAY DIFFRACTION97
1.2563-1.28050.17531770.14533363X-RAY DIFFRACTION97
1.2805-1.30660.15451800.13413417X-RAY DIFFRACTION98
1.3066-1.3350.14881820.13273456X-RAY DIFFRACTION98
1.335-1.36610.15481810.13373444X-RAY DIFFRACTION98
1.3661-1.40020.16211790.13063408X-RAY DIFFRACTION98
1.4002-1.43810.15971840.13173497X-RAY DIFFRACTION99
1.4381-1.48040.15341840.12473504X-RAY DIFFRACTION99
1.4804-1.52820.16161830.12553473X-RAY DIFFRACTION100
1.5282-1.58280.13781840.12013491X-RAY DIFFRACTION100
1.5828-1.64620.13341850.1213519X-RAY DIFFRACTION100
1.6462-1.72110.14281830.13213480X-RAY DIFFRACTION100
1.7211-1.81180.14931870.13433546X-RAY DIFFRACTION100
1.8118-1.92530.17271830.14163488X-RAY DIFFRACTION99
1.9253-2.0740.1451850.14583507X-RAY DIFFRACTION99
2.074-2.28270.16871850.14743517X-RAY DIFFRACTION100
2.2827-2.61290.1671850.15893520X-RAY DIFFRACTION99
2.6129-3.29160.15311870.1613546X-RAY DIFFRACTION99
3.2916-35.06950.16541880.14183561X-RAY DIFFRACTION98

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