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

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Basic information

Entry
Database: PDB / ID: 4yxu
TitleHuman Carbonic Anhydrase II complexed with an inhibitor with a benzenesulfonamide group (4).
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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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-propylbenzenesulfonamide / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 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)30,1676
Polymers29,2891
Non-polymers8785
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-12 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.437, 41.741, 72.239
Angle α, β, γ (deg.)90.00, 104.26, 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, 249 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-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-4JE / 4-propylbenzenesulfonamide


Mass: 199.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13NO2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 40.81 %
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: Dec 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.08→50 Å / Num. obs: 103099 / % possible obs: 98 % / Redundancy: 3.28 % / Biso Wilson estimate: 7.703 Å2 / Rsym value: 0.055 / Net I/σ(I): 12.07
Reflection shellResolution: 1.08→1.15 Å / Redundancy: 3.18 % / Mean I/σ(I) obs: 2.64 / % possible all: 95

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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: 1.08→41.129 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1633 5154 5 %Random selection
Rwork0.1441 ---
obs0.1451 103095 98.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.08→41.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 43 244 2321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052231
X-RAY DIFFRACTIONf_angle_d1.13045
X-RAY DIFFRACTIONf_dihedral_angle_d11.915820
X-RAY DIFFRACTIONf_chiral_restr0.079314
X-RAY DIFFRACTIONf_plane_restr0.005415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0797-1.0920.21431610.20493064X-RAY DIFFRACTION92
1.092-1.10480.1971640.19263116X-RAY DIFFRACTION95
1.1048-1.11830.18561680.18513202X-RAY DIFFRACTION96
1.1183-1.13250.1861660.17033146X-RAY DIFFRACTION96
1.1325-1.14740.18251690.16773210X-RAY DIFFRACTION96
1.1474-1.16310.20361670.16673165X-RAY DIFFRACTION95
1.1631-1.17970.16821680.15543199X-RAY DIFFRACTION96
1.1797-1.19730.18511690.15613222X-RAY DIFFRACTION97
1.1973-1.2160.18491710.14983239X-RAY DIFFRACTION97
1.216-1.2360.15961680.14453198X-RAY DIFFRACTION98
1.236-1.25730.18291720.14283257X-RAY DIFFRACTION98
1.2573-1.28010.15961710.14043260X-RAY DIFFRACTION98
1.2801-1.30480.13491740.133292X-RAY DIFFRACTION99
1.3048-1.33140.1511710.12733259X-RAY DIFFRACTION99
1.3314-1.36030.15521720.13483266X-RAY DIFFRACTION99
1.3603-1.3920.17911740.1313309X-RAY DIFFRACTION99
1.392-1.42680.13961720.13133275X-RAY DIFFRACTION99
1.4268-1.46540.14691730.1253282X-RAY DIFFRACTION99
1.4654-1.50850.13391730.12363288X-RAY DIFFRACTION99
1.5085-1.55720.15491740.12163307X-RAY DIFFRACTION99
1.5572-1.61290.15761750.12633325X-RAY DIFFRACTION100
1.6129-1.67740.13931750.12963311X-RAY DIFFRACTION99
1.6774-1.75380.15241740.12693323X-RAY DIFFRACTION100
1.7538-1.84620.13891750.13553322X-RAY DIFFRACTION100
1.8462-1.96190.13841750.13453311X-RAY DIFFRACTION100
1.9619-2.11340.17061770.14063363X-RAY DIFFRACTION100
2.1134-2.32610.1631750.14583326X-RAY DIFFRACTION99
2.3261-2.66260.17331750.15753331X-RAY DIFFRACTION99
2.6626-3.35430.17281770.15613361X-RAY DIFFRACTION99
3.3543-41.15870.16891790.14543412X-RAY DIFFRACTION98

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