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- PDB-7yzh: Schistosoma Mansoni Carbonic Anhydrase in complex with 4-oxo-N-(4... -

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Basic information

Entry
Database: PDB / ID: 7yzh
TitleSchistosoma Mansoni Carbonic Anhydrase in complex with 4-oxo-N-(4-sulfamoylphenethyl)-1,3,4,6,7,11b-hexahydro-2H-pyrazino[2,1-a]isoquinoline-2-carbothioamide
ComponentsCarbonic anhydrase
KeywordsLYASE / Schistosoma mansoni / carbonic anhydrase / sulfonamide / / metalloenzyme
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / zinc ion binding / plasma membrane
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-HFF / Carbonic anhydrase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsAngeli, A. / Ferraroni, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Enzyme Inhib Med Chem / Year: 2022
Title: Development of Praziquantel sulphonamide derivatives as antischistosomal drugs.
Authors: Angeli, A. / Ferraroni, M. / Carta, F. / Haberli, C. / Keiser, J. / Costantino, G. / Supuran, C.T.
History
DepositionFeb 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Carbonic anhydrase
BBB: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,19412
Polymers73,9762
Non-polymers2,21810
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint12 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.830, 103.830, 133.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Sugars , 2 types, 7 molecules AAABBB

#1: Protein Carbonic anhydrase


Mass: 36988.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A3Q0KSG2, carbonic anhydrase
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 376 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HFF / 4-oxo-N-(4-sulfamoylphenethyl)-1,3,4,6,7,11b-hexahydro-2H-pyrazino[2,1-a]isoquinoline-2-carbothioamide / (11b-R)-4-oxidanylidene-N-[2-(4-sulfamoylphenyl)ethyl]-3,6,7,11b-tetrahydro-1H-pyrazino[2,1-a]isoquinoline-2-carbothioamide


Mass: 444.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24N4O3S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 6000, 0.1 M citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.79→48 Å / Num. obs: 79049 / % possible obs: 100 % / Redundancy: 19.13 % / CC1/2: 1 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.089 / Net I/σ(I): 24.04
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 17.97 % / Rmerge(I) obs: 1.455 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 5786 / CC1/2: 0.81 / Rrim(I) all: 1.497 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QQM

6qqm


Resolution: 1.79→48 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.118 / SU ML: 0.065 / Cross valid method: NONE / ESU R: 0.092 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.198 3862 4.886 %
Rwork0.1679 75187 -
all0.169 --
obs-79049 99.979 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.417 Å2
Baniso -1Baniso -2Baniso -3
1-0.286 Å20.143 Å20 Å2
2--0.286 Å2-0 Å2
3----0.926 Å2
Refinement stepCycle: LAST / Resolution: 1.79→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4474 0 138 371 4983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134772
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154313
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.6666514
X-RAY DIFFRACTIONr_angle_other_deg1.4151.6069937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4195563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.72421.977258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34515746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4751531
X-RAY DIFFRACTIONr_chiral_restr0.0850.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021166
X-RAY DIFFRACTIONr_nbd_refined0.2260.2795
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.24212
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22346
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22190
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2275
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3050.29
X-RAY DIFFRACTIONr_nbd_other0.2440.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.211
X-RAY DIFFRACTIONr_mcbond_it2.7873.0392226
X-RAY DIFFRACTIONr_mcbond_other2.7683.0262221
X-RAY DIFFRACTIONr_mcangle_it3.5554.5352779
X-RAY DIFFRACTIONr_mcangle_other3.5494.5352779
X-RAY DIFFRACTIONr_scbond_it4.1783.542546
X-RAY DIFFRACTIONr_scbond_other4.1773.5412547
X-RAY DIFFRACTIONr_scangle_it6.0745.1813729
X-RAY DIFFRACTIONr_scangle_other6.0745.1813730
X-RAY DIFFRACTIONr_lrange_it7.05936.915207
X-RAY DIFFRACTIONr_lrange_other7.05836.9155208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.8320.2642990.2365484X-RAY DIFFRACTION99.7757
1.832-1.8830.2632730.2155359X-RAY DIFFRACTION99.9822
1.883-1.9370.2272530.215217X-RAY DIFFRACTION100
1.937-1.9970.242720.1885098X-RAY DIFFRACTION100
1.997-2.0620.1952390.1844888X-RAY DIFFRACTION100
2.062-2.1350.2322760.1784775X-RAY DIFFRACTION100
2.135-2.2150.232130.1794625X-RAY DIFFRACTION100
2.215-2.3050.2262380.1734409X-RAY DIFFRACTION100
2.305-2.4080.2132120.1684261X-RAY DIFFRACTION100
2.408-2.5250.2252150.1624060X-RAY DIFFRACTION100
2.525-2.6620.1952130.1553863X-RAY DIFFRACTION100
2.662-2.8230.2011860.163688X-RAY DIFFRACTION100
2.823-3.0180.1861920.1683443X-RAY DIFFRACTION100
3.018-3.2590.2081560.1773237X-RAY DIFFRACTION100
3.259-3.570.1991420.1743009X-RAY DIFFRACTION100
3.57-3.9910.1881390.1542715X-RAY DIFFRACTION100
3.991-4.6060.1451270.1282397X-RAY DIFFRACTION100
4.606-5.6380.149960.1372068X-RAY DIFFRACTION100
5.638-7.9580.226660.1811649X-RAY DIFFRACTION100
7.958-480.19550.21942X-RAY DIFFRACTION99.7

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