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- PDB-7agn: Human carbonic anhydrase II in complex with 4-(2-aminoethylsulfan... -

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Basic information

Entry
Database: PDB / ID: 7agn
TitleHuman carbonic anhydrase II in complex with 4-(2-aminoethylsulfanyl)-2,3,5,6-tetrafluoro-N-methyl-benzenesulfonamide
Componentscarbonic anhydrase 2
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex
Function / homology
Function and homology information


positive regulation of dipeptide transmembrane transport / positive regulation of cellular pH reduction / Developmental Lineage of Pancreatic Ductal Cells / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide ...positive regulation of dipeptide transmembrane transport / positive regulation of cellular pH reduction / Developmental Lineage of Pancreatic Ductal Cells / 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 / cytoplasm / cytosol
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
Chem-RAK / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsPaketuryte, V. / Smirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Eur.Biophys.J. / Year: 2021
Title: Structure and mechanism of secondary sulfonamide binding to carbonic anhydrases.
Authors: Baronas, D. / Dudutiene, V. / Paketuryte, V. / Kairys, V. / Smirnov, A. / Juozapaitiene, V. / Vaskevicius, A. / Manakova, E. / Grazulis, S. / Zubriene, A. / Matulis, D.
History
DepositionSep 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: carbonic anhydrase 2
B: carbonic anhydrase 2
C: carbonic anhydrase 2
D: carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,43620
Polymers117,1564
Non-polymers2,28016
Water24,0681336
1
A: carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8595
Polymers29,2891
Non-polymers5704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8826
Polymers29,2891
Non-polymers5935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8364
Polymers29,2891
Non-polymers5473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8595
Polymers29,2891
Non-polymers5704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.888, 41.141, 84.258
Angle α, β, γ (deg.)90.000, 109.510, 90.000
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
carbonic anhydrase 2


Mass: 29289.062 Da / Num. of mol.: 4
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 , 5 types, 1352 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-RAK / 4-(2-azanylethylsulfanyl)-2,3,5,6-tetrakis(fluoranyl)-~{N}-methyl-benzenesulfonamide


Mass: 318.312 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H10F4N2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1336 / 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: 40.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.147→79.421 Å / Num. all: 296762 / Num. obs: 296762 / % possible obs: 88.6 % / Redundancy: 3.6 % / Rpim(I) all: 0.068 / Rrim(I) all: 0.132 / Rsym value: 0.102 / Net I/av σ(I): 1.9 / Net I/σ(I): 4.3 / Num. measured all: 1062546
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
1.15-1.213.30.342.2110526330650.2570.490.341.667.5
1.21-1.283.60.2722.7147646413700.1980.3830.2722.189.4
1.28-1.373.50.2073.4139515393730.1520.2920.2072.690.4
1.37-1.483.60.1574.3133652369270.1150.2220.1573.291.4
1.48-1.623.60.125.3122227342190.0880.170.124.192
1.62-1.813.70.1045.8115453313890.0750.1450.1045.293.3
1.81-2.093.60.0935.9100874278740.0660.1270.0936.793.8
2.09-2.573.70.0915.987946238840.0620.1190.0917.895
2.57-3.633.70.0954.667517184550.0620.1190.0958.895.6
3.63-79.4213.60.101437190102060.0650.1250.1018.796.3

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT0

4ht0


Resolution: 1.15→69.65 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 29196 9.9 %RANDOM
Rwork0.1474 ---
obs0.1512 265110 87.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 167.85 Å2 / Biso mean: 16.849 Å2 / Biso min: 4.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0.38 Å20.03 Å2
2--0.02 Å2-0.01 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 1.15→69.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8178 0 128 1342 9648
Biso mean--21.26 30.18 -
Num. residues----1032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0199098
X-RAY DIFFRACTIONr_angle_refined_deg2.2331.95612459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22651141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60624.765426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09151446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5741530
X-RAY DIFFRACTIONr_chiral_restr0.1860.21279
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0217235
X-RAY DIFFRACTIONr_rigid_bond_restr5.69939098
X-RAY DIFFRACTIONr_sphericity_free26.7495792
X-RAY DIFFRACTIONr_sphericity_bonded13.90459346
LS refinement shellResolution: 1.15→1.177 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.309 1150 -
Rwork0.3 10642 -
obs--47.5 %

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