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- PDB-5dog: Crystal structure of human carbonic anhydrase isozyme II with 2-(... -

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Basic information

Entry
Database: PDB / ID: 5dog
TitleCrystal structure of human carbonic anhydrase isozyme II with 2-(Benzylamino)-3,5,6-trifluoro-4-[(2-phenylethyl)thio]benzene- sulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase 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 / 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
Chem-5DT / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: ChemMedChem / Year: 2017
Title: Intrinsic Thermodynamics and Structures of 2,4- and 3,4-Substituted Fluorinated Benzenesulfonamides Binding to Carbonic Anhydrases.
Authors: Zubriene, A. / Smirnov, A. / Dudutiene, V. / Timm, D.D. / Matuliene, J. / Michailoviene, V. / Zaksauskas, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionSep 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Jan 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)30,1655
Polymers29,2891
Non-polymers8764
Water5,296294
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint8 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.228, 41.249, 72.351
Angle α, β, γ (deg.)90.000, 104.290, 90.000
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 / Fragment: human carbonic anhydrase II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 298 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Fragment: 2-[(2-Phenylethyl)amino]-3,5,6-trifluoro-4-[(2-phenylethyl)thio]-benzenesulfonamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Fragment: Zn / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Fragment: BICINE / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-5DT / 2-(benzylamino)-3,5,6-trifluoro-4-[(2-phenylethyl)sulfanyl]benzenesulfonamide


Mass: 452.513 Da / Num. of mol.: 1 / Fragment: N-(EHTYLSULFITE)MORPHOLINE / Source method: obtained synthetically / Formula: C21H19F3N2O2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallization buffer: 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 8, 2012
RadiationMonochromator: VARIMAX-HF MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→22.871 Å / Num. all: 26789 / Num. obs: 26789 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.023 Å2 / Rpim(I) all: 0.026 / Rrim(I) all: 0.049 / Rsym value: 0.031 / Net I/av σ(I): 11.548 / Net I/σ(I): 18.6 / Num. measured all: 94591
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.7-1.793.40.2310.1553.61304838580.120.230.15516.699.2
1.79-1.93.50.1180.0837.31286436790.060.120.08310.199.9
1.9-2.033.50.0820.05311.11209434520.040.080.05313.7100
2.03-2.193.60.0650.03913.91154032430.030.060.03917.6100
2.19-2.43.60.0550.03316.41052529460.030.050.03320.6100
2.4-2.693.60.0470.02819.8978827100.030.050.02822.5100
2.69-3.13.60.0380.02422.5867923960.020.040.02426.9100
3.1-3.83.60.0430.02813.7734420230.020.040.02831.4100
3.8-5.383.60.0350.02321.1571615930.020.040.02334.2100
5.38-22.873.40.0340.02119.929938890.020.030.02129.898.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
REFMAC5.6.0117refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLJ

3hlj


Resolution: 1.7→22.87 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.169 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.887 / SU R Cruickshank DPI: 0.119 / SU Rfree: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2737 10.2 %RANDOM
Rwork0.162 24041 --
obs0.167 26778 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.71 Å2 / Biso mean: 16.753 Å2 / Biso min: 5.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0.07 Å2
2--0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 50 294 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022227
X-RAY DIFFRACTIONr_angle_refined_deg2.3021.9873028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9935265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31924.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16215355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.14157
X-RAY DIFFRACTIONr_chiral_restr0.1610.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211734
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 200 -
Rwork0.349 1734 -
all-1934 -
obs--99.03 %

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