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- PDB-7nwy: Crystal structure of alpha carbonic anhydrase from schistosoma ma... -

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Basic information

Entry
Database: PDB / ID: 7nwy
TitleCrystal structure of alpha carbonic anhydrase from schistosoma mansoni with 4-(3-(4-fluorophenyl)ureido)benzenesulfonamide
ComponentsCarbonic anhydrase
KeywordsLYASE / schistosoma mansoni / carbonic anhydrase / metalloenzyme / inhibitor / neglected diseases / sulfonamide
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-WWZ / Carbonic anhydrase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.807 Å
AuthorsAngeli, A. / Ferraroni, M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structural Insights into Schistosoma mansoni Carbonic Anhydrase (SmCA) Inhibition by Selenoureido-Substituted Benzenesulfonamides.
Authors: Angeli, A. / Ferraroni, M. / Da'dara, A.A. / Selleri, S. / Pinteala, M. / Carta, F. / Skelly, P.J. / Supuran, C.T.
History
DepositionMar 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: 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
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3Nov 13, 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)73,35712
Polymers71,4102
Non-polymers1,94810
Water5,441302
1
BBB: Carbonic anhydrase
hetero molecules

AAA: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,35712
Polymers71,4102
Non-polymers1,94810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_454-x-1,-x+y,-z-1/31
Buried area4190 Å2
ΔGint2 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.480, 103.480, 132.500
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: 35704.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Schistosoma mansoni (invertebrata) / 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, 307 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-WWZ / 4-{[(4-fluorophenyl)carbamoyl]amino}benzenesulfonamide


Mass: 309.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12FN3O3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Citrate pH 5.0; 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.807→53.33 Å / Num. obs: 73383 / % possible obs: 97.1 % / Redundancy: 17.33 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.089 / Net I/σ(I): 20.77
Reflection shellResolution: 1.807→1.99 Å / Mean I/σ(I) obs: 2.25 / Num. unique obs: 5517 / CC1/2: 0.81 / % possible all: 100

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Processing

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

6qqm


Resolution: 1.807→53.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.65 / SU ML: 0.078 / Cross valid method: NONE / ESU R: 0.114 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2264 3591 4.975 %
Rwork0.1904 68584 -
all0.192 --
obs-72175 95.519 %
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: 31.419 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å2-0.002 Å2-0 Å2
2---0.003 Å20 Å2
3---0.011 Å2
Refinement stepCycle: LAST / Resolution: 1.807→53.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 120 302 4901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134815
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174341
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.6686584
X-RAY DIFFRACTIONr_angle_other_deg1.4271.59610010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6415579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02722.197264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6415760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3311530
X-RAY DIFFRACTIONr_chiral_restr0.0880.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025642
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021184
X-RAY DIFFRACTIONr_nbd_refined0.2030.2855
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.24351
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22394
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2470.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.210
X-RAY DIFFRACTIONr_nbd_other0.1850.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.211
X-RAY DIFFRACTIONr_mcbond_it2.8353.0932246
X-RAY DIFFRACTIONr_mcbond_other2.8353.0942247
X-RAY DIFFRACTIONr_mcangle_it3.624.6232808
X-RAY DIFFRACTIONr_mcangle_other3.624.6222808
X-RAY DIFFRACTIONr_scbond_it4.0573.4982569
X-RAY DIFFRACTIONr_scbond_other4.0563.4982570
X-RAY DIFFRACTIONr_scangle_it5.9685.1083762
X-RAY DIFFRACTIONr_scangle_other5.9675.1073763
X-RAY DIFFRACTIONr_lrange_it7.12837.0955372
X-RAY DIFFRACTIONr_lrange_other7.13437.1325357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.807-1.8540.282930.2415223X-RAY DIFFRACTION99.9819
1.854-1.9050.3571460.3193202X-RAY DIFFRACTION61.8854
1.905-1.960.5762380.5134199X-RAY DIFFRACTION85.1141
1.96-2.020.2131970.1894915X-RAY DIFFRACTION100
2.02-2.0860.2122400.1774688X-RAY DIFFRACTION100
2.086-2.1590.2142520.1684570X-RAY DIFFRACTION100
2.159-2.2410.3352130.3354091X-RAY DIFFRACTION93.423
2.241-2.3320.4092370.3343970X-RAY DIFFRACTION94.6883
2.332-2.4360.2162300.1644049X-RAY DIFFRACTION100
2.436-2.5550.1941940.1583890X-RAY DIFFRACTION100
2.555-2.6930.22350.1713656X-RAY DIFFRACTION100
2.693-2.8560.2172090.1673508X-RAY DIFFRACTION100
2.856-3.0530.1971590.1713314X-RAY DIFFRACTION100
3.053-3.2970.2021550.1773101X-RAY DIFFRACTION100
3.297-3.6120.1831380.1692847X-RAY DIFFRACTION99.9665
3.612-4.0370.1711100.1652611X-RAY DIFFRACTION99.9633
4.037-4.660.1421100.1192331X-RAY DIFFRACTION100
4.66-5.7030.191140.1431951X-RAY DIFFRACTION100
5.703-8.050.214690.1781565X-RAY DIFFRACTION99.9388
8-100.217520.217903X-RAY DIFFRACTION99.4792

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