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- PDB-6t4n: Human Carbonic anhydrase II bound by 2,4,6-trimethylbenzenesulfonamide -

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Basic information

Entry
Database: PDB / ID: 6t4n
TitleHuman Carbonic anhydrase II bound by 2,4,6-trimethylbenzenesulfonamide
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, 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
Similarity search - Domain/homology
2,4,6-trimethylbenzenesulfonamide / 2-piperazin-1-ylethanol / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Biophys.J. / Year: 2020
Title: Isoform-Selective Enzyme Inhibitors by Exploring Pocket Size According to the Lock-and-Key Principle.
Authors: Dudutiene, V. / Zubriene, A. / Kairys, V. / Smirnov, A. / Smirnoviene, J. / Leitans, J. / Kazaks, A. / Tars, K. / Manakova, L. / Grazulis, S. / Matulis, D.
History
DepositionOct 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 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)29,9256
Polymers29,2891
Non-polymers6365
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint4 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.115, 41.106, 71.861
Angle α, β, γ (deg.)90.000, 104.140, 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


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) / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 6 types, 308 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-F1A / 2,4,6-trimethylbenzenesulfonamide


Mass: 199.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical ChemComp-MJB / 2-piperazin-1-ylethanol


Mass: 130.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Crystallization buffer was 0.1M sodium BICINE, pH 9, 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9768 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 1.4→69.683 Å / Num. all: 46739 / Num. obs: 46739 / % possible obs: 99.1 % / Redundancy: 6.4 % / Rpim(I) all: 0.016 / Rrim(I) all: 0.04 / Rsym value: 0.032 / Net I/av σ(I): 12 / Net I/σ(I): 26.1 / Num. measured all: 301331
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.4-1.4860.2243.34032067040.1060.2640.2246.898.5
1.48-1.576.20.14853965464370.070.1760.1489.699.1
1.57-1.676.30.1017.33752260030.0480.1220.10113.399
1.67-1.816.40.06810.63602556370.0330.0850.06818.199.1
1.81-1.986.70.04615.33488251890.0220.0580.04626.399.4
1.98-2.216.80.03419.53213647100.0170.0440.0343699.3
2.21-2.566.80.03219.72842541850.0160.0410.03242.399.2
2.56-3.136.80.02623.62400735360.0130.0340.02650.899.6
3.13-4.436.50.02323.41803127610.0110.0290.02361.799.6
4.43-69.6836.50.02321.81032915770.0120.030.02361.899.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT0

4ht0


Resolution: 1.4→40.84 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.069
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 4199 9 %RANDOM
Rwork0.1697 ---
obs0.1723 42514 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 65.17 Å2 / Biso mean: 17.946 Å2 / Biso min: 7.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å2-0.11 Å2
2---0.67 Å20 Å2
3---0.52 Å2
Refinement stepCycle: final / Resolution: 1.4→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 38 304 2385
Biso mean--29.12 29.19 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122294
X-RAY DIFFRACTIONr_angle_refined_deg1.991.6493134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4025287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53423.739115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17315368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.443158
X-RAY DIFFRACTIONr_chiral_restr0.130.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021822
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.227 3391 -
obs--98.43 %

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