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- PDB-9fps: Crystal structure of carbonic anhydrase II with methyl 4-methylsu... -

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Basic information

Entry
Database: PDB / ID: 9fps
TitleCrystal structure of carbonic anhydrase II with methyl 4-methylsulfanyl-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 / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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: 1.39 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)29,9555
Polymers29,2891
Non-polymers6664
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-29 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.314, 41.169, 72.026
Angle α, β, γ (deg.)90.000, 104.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1IEM / methyl 4-methylsulfanyl-3-sulfamoyl-benzoate


Mass: 261.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium bicine (pH 9) 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: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.39→40.985 Å / Num. all: 47284 / Num. obs: 47284 / % possible obs: 97.6 % / Redundancy: 7 % / Rpim(I) all: 0.017 / Rrim(I) all: 0.044 / Rsym value: 0.036 / Net I/av σ(I): 8.9 / Net I/σ(I): 24.2 / Num. measured all: 329733
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
1.39-1.476.80.3771.94561166910.1680.4430.3774.794.9
1.47-1.5570.1993.54483764110.0880.2360.1997.996.8
1.55-1.6670.125.84245860640.0550.1460.1211.896.9
1.66-1.7970.0769.14037957340.0350.0940.07616.998.3
1.79-1.977.10.0513.43756353090.0230.0630.0524.998.6
1.97-2.26.90.03618.43300447580.0170.0460.03633.498.2
2.2-2.546.90.03212931942430.0150.0390.0340.298.5
2.54-3.117.10.028222597136470.0130.0350.02848.399.5
3.11-4.46.90.02719.61953928240.0120.0330.02758.499.1
4.4-40.9856.90.03213.51105216030.0150.0390.0325899.2

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→39.94 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 4706 10 %RANDOM
Rwork0.1416 ---
obs0.1464 42563 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 103.53 Å2 / Biso mean: 21.784 Å2 / Biso min: 10.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å2-0 Å20.98 Å2
2---0.45 Å20 Å2
3----1.12 Å2
Refinement stepCycle: final / Resolution: 1.39→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 37 344 2422
Biso mean--23.88 35.25 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122223
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.6523039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0165276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71223.796108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63815354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.657157
X-RAY DIFFRACTIONr_chiral_restr0.1330.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021762
X-RAY DIFFRACTIONr_rigid_bond_restr4.96932223
X-RAY DIFFRACTIONr_sphericity_free29.45198
X-RAY DIFFRACTIONr_sphericity_bonded17.19252298
LS refinement shellResolution: 1.39→1.426 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 319 -
Rwork0.411 3010 -
all-3329 -
obs--92.83 %

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