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- PDB-7qzx: Human Carbonic Anhydrase II in complex with 4-oxo-N-(4-sulfamoylp... -

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Basic information

Entry
Database: PDB / ID: 7qzx
TitleHuman Carbonic Anhydrase II in complex with 4-oxo-N-(4-sulfamoylphenethyl)-1,3,4,6,7,11b-hexahydro-2H-pyrazino[2,1-a]isoquinoline-2-carboxamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase II / inhibitor / metalloenzyme / praziquantel / sulfonamide
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 / cyanamide hydratase activity / 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 / 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 / cytosol / cytoplasm
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-HIL / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 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 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8754
Polymers29,2891
Non-polymers5863
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-7 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.470, 41.770, 72.100
Angle α, β, γ (deg.)90.000, 104.491, 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-HIL / 4-oxo-N-(4-sulfamoylphenethyl)-1,3,4,6,7,11b-hexahydro-2H-pyrazino[2,1-a]isoquinoline-2-carboxamide / (11b-R)-4-oxidanylidene-N-[2-(4-sulfamoylphenyl)ethyl]-3,6,7,11b-tetrahydro-1H-pyrazino[2,1-a]isoquinoline-2-carboxamide


Mass: 428.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N4O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5 M sodium citrate, 0.1 M Tris pH 8.0

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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: Feb 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.24→41.153 Å / Num. obs: 62450 / % possible obs: 88.8 % / Redundancy: 6.17 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.071 / Net I/σ(I): 13.84
Reflection shellResolution: 1.24→1.27 Å / Redundancy: 4.56 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 2417 / CC1/2: 0.766 / Rrim(I) all: 0.732 / % possible all: 46.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIK

4fik


Resolution: 1.24→41.153 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.641 / SU ML: 0.028 / Cross valid method: NONE / ESU R: 0.045 / ESU R Free: 0.046
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.179 3082 4.935 %
Rwork0.1588 59368 -
all0.16 --
obs-62450 88.772 %
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: 16.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å2-0.112 Å2
2--0.419 Å2-0 Å2
3---0.113 Å2
Refinement stepCycle: LAST / Resolution: 1.24→41.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 37 225 2312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132158
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161977
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.6332933
X-RAY DIFFRACTIONr_angle_other_deg1.4721.6044582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0635258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21623.645107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9115346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.231157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022504
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
X-RAY DIFFRACTIONr_nbd_refined0.2480.2391
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.21888
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21031
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21023
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2130
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1230.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0580.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2670.214
X-RAY DIFFRACTIONr_nbd_other0.2580.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.226
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0910.21
X-RAY DIFFRACTIONr_mcbond_it1.6711.4821034
X-RAY DIFFRACTIONr_mcbond_other1.6511.4761031
X-RAY DIFFRACTIONr_mcangle_it2.4762.2241288
X-RAY DIFFRACTIONr_mcangle_other2.4732.2241288
X-RAY DIFFRACTIONr_scbond_it2.7381.7451124
X-RAY DIFFRACTIONr_scbond_other2.7371.7451125
X-RAY DIFFRACTIONr_scangle_it4.0412.511644
X-RAY DIFFRACTIONr_scangle_other4.042.5091645
X-RAY DIFFRACTIONr_lrange_it4.92318.232379
X-RAY DIFFRACTIONr_lrange_other4.86117.8372338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.2670.2661270.2532287X-RAY DIFFRACTION46.2629
1.267-1.3020.2621460.2292805X-RAY DIFFRACTION58.914
1.302-1.340.2332050.2163636X-RAY DIFFRACTION78.7574
1.34-1.3810.2342220.1944176X-RAY DIFFRACTION92.3755
1.381-1.4260.1972310.1764170X-RAY DIFFRACTION95.054
1.426-1.4760.1772030.1614050X-RAY DIFFRACTION95.616
1.476-1.5320.1772040.1593926X-RAY DIFFRACTION95.4251
1.532-1.5950.1472100.143780X-RAY DIFFRACTION96.0751
1.595-1.6660.1881630.1443716X-RAY DIFFRACTION96.709
1.666-1.7470.1771910.1523450X-RAY DIFFRACTION95.6899
1.747-1.8410.1721960.1533327X-RAY DIFFRACTION97.1326
1.841-1.9530.1571270.1473219X-RAY DIFFRACTION97.409
1.953-2.0870.171530.1533010X-RAY DIFFRACTION97.6536
2.087-2.2550.1671250.1522802X-RAY DIFFRACTION97.0491
2.255-2.470.1651180.1482618X-RAY DIFFRACTION98.3112
2.47-2.7610.2051340.1582347X-RAY DIFFRACTION98.4524
2.761-3.1870.191000.1662101X-RAY DIFFRACTION98.6111
3.187-3.9010.195860.1491795X-RAY DIFFRACTION98.792
3.901-5.5080.142960.1421365X-RAY DIFFRACTION98.6496
5.508-41.1530.186450.186788X-RAY DIFFRACTION97.77

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