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- PDB-9fpq: Crystal structure of carbonic anhydrase II with methyl 4-benzylsu... -

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Basic information

Entry
Database: PDB / ID: 9fpq
TitleCrystal structure of carbonic anhydrase II with methyl 4-benzylsulfanyl-3-sulfamoyl-benzoate
ComponentsCarbonic anhydrase 2
KeywordsLYASE / DRUG DESIGN / CARBONIC ANHYDRASE / BENZENESULFONAMIDE / 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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / 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
: / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSmirnov, A. / Manakova, E.N. / Grazulis, S. / Paketuryte, V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Affinity and Selectivity of Protein-Ligand Recognition: A Minor Chemical Modification Changes Carbonic Anhydrase Binding Profile.
Authors: Zaksauskas, A. / Paketuryte-Latve, V. / Jankunaite, A. / Capkauskaite, E. / Becart, Y. / Smirnov, A. / Pospisilova, K. / Leitans, J. / Brynda, J. / Kazaks, A. / Baranauskiene, L. / Manakova, ...Authors: Zaksauskas, A. / Paketuryte-Latve, V. / Jankunaite, A. / Capkauskaite, E. / Becart, Y. / Smirnov, A. / Pospisilova, K. / Leitans, J. / Brynda, J. / Kazaks, A. / Baranauskiene, L. / Manakova, E. / Grazulis, S. / Kairys, V. / Tars, K. / Rezacova, P. / Matulis, D.
History
DepositionJun 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)29,9335
Polymers29,2891
Non-polymers6444
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint3 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.302, 41.279, 72.213
Angle α, β, γ (deg.)90.000, 104.210, 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
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, 269 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1IEL / methyl 4-(phenylmethylsulfanyl)-3-sulfamoyl-benzoate


Mass: 337.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15NO4S2 / 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-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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
Details: 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / 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: 1.5→70.002 Å / Num. all: 38824 / Num. obs: 38824 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Rsym value: 0.049 / Net I/av σ(I): 8.6 / Net I/σ(I): 15.9 / Num. measured all: 258122
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
1.5-1.586.40.2482.93575156050.1120.2880.2484.999.2
1.58-1.686.70.1813.93608353530.080.2110.1816.5100
1.68-1.796.70.1335.23375050440.0590.1550.1338.399.9
1.79-1.946.30.0986.82890846250.0450.1160.09811.199.1
1.94-2.1270.0729.13042843350.0320.0840.07216.699.9
2.12-2.376.90.06110.72691538980.0270.0720.06120.699.8
2.37-2.746.30.05811.12154834280.0270.0690.05822.799.2
2.74-3.3570.04514.42075029460.020.0530.04531.8100
3.35-4.746.70.03418.31538322860.0150.0390.03439.499.7
4.74-70.0026.60.03215.9860613040.0150.0390.0323799.7

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
Cootmodel building
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→70 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 4014 10.4 %RANDOM
Rwork0.169 ---
obs0.172 34677 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.26 Å2 / Biso mean: 21.583 Å2 / Biso min: 10.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.31 Å2
2---1 Å20 Å2
3---0.89 Å2
Refinement stepCycle: final / Resolution: 1.5→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 38 265 2351
Biso mean--31.56 32.62 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122221
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.6493025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9815272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66523.738107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58215357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.333157
X-RAY DIFFRACTIONr_chiral_restr0.1250.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021744
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 281 -
Rwork0.185 2518 -
all-2799 -
obs--97.56 %

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