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- PDB-6g6t: Crystal structure of human carbonic anhydrase isozyme II with N-b... -

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Basic information

Entry
Database: PDB / ID: 6g6t
TitleCrystal structure of human carbonic anhydrase isozyme II with N-butyl-2,4-dichloro-5-sulfamoyl-benzamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor comple
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 / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / zinc ion binding / extracellular exosome / 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
Chem-ENN / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.12 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Eur J Med Chem / Year: 2018
Title: Design of two-tail compounds with rotationally fixed benzenesulfonamide ring as inhibitors of carbonic anhydrases.
Authors: Zaksauskas, A. / Capkauskaite, E. / Jezepcikas, L. / Linkuviene, V. / Kisonaite, M. / Smirnov, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionApr 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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)29,9215
Polymers29,2891
Non-polymers6324
Water5,909328
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint4 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.057, 41.196, 72.094
Angle α, β, γ (deg.)90.000, 104.190, 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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 332 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Mutation: N-butyl-2,4-dichloro-5-sulfamoyl-benzamide / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Fragment: Zn / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Fragment: Bicine / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical ChemComp-ENN / ~{N}-butyl-2,4-bis(chloranyl)-5-sulfamoyl-benzamide


Mass: 325.211 Da / Num. of mol.: 1 / Fragment: Dimethyl sulfoxide / Source method: obtained synthetically / Formula: C11H14Cl2N2O3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.07 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallization buffer: 0.1M sodium bicine (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.975522 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975522 Å / Relative weight: 1
ReflectionResolution: 1.12→41.196 Å / Num. obs: 86201 / % possible obs: 94.3 % / Redundancy: 6.4 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.066 / Rsym value: 0.052 / Net I/av σ(I): 3.664 / Net I/σ(I): 28.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.123-1.1850.064110.0380.0890.06473.4
1.18-1.265.80.05812.30.0320.0810.05894.2
1.26-1.346.70.05213.90.0280.0720.05298.4
1.34-1.456.60.04416.20.0240.0630.04498.6
1.45-1.596.70.03718.50.0210.0550.03798.1
1.59-1.786.70.03320.50.0180.0480.03398.7
1.78-2.056.90.0321.80.0150.0410.0399.2
2.05-2.516.90.0318.40.0150.0390.0399
2.51-3.556.90.0498.10.0220.0590.04999.2
3.55-41.1966.60.0836.60.0390.1020.08398.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT0

4ht0


Resolution: 1.12→39.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.0365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.038
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 8706 10.1 %RANDOM
Rwork0.1433 ---
obs0.1467 86179 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 143.74 Å2 / Biso mean: 16.1384 Å2 / Biso min: 5.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20.07 Å2
2---0.53 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.12→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 35 328 2397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192265
X-RAY DIFFRACTIONr_angle_refined_deg2.8371.9613092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3524.66103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9115371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.48158
X-RAY DIFFRACTIONr_chiral_restr0.1850.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0211781
X-RAY DIFFRACTIONr_mcbond_it2.3431.2061097
X-RAY DIFFRACTIONr_mcangle_it2.5021.8231391
X-RAY DIFFRACTIONr_scbond_it3.7421.5041168
X-RAY DIFFRACTIONr_rigid_bond_restr10.83932265
X-RAY DIFFRACTIONr_sphericity_free22.3625170
X-RAY DIFFRACTIONr_sphericity_bonded14.82352351
LS refinement shellResolution: 1.123→1.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.183 415 -
Rwork0.138 3793 -
all-4208 -
obs--62.41 %

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