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- PDB-7r1x: human Carbonic Anhydrase II in complex with 4-oxo-N-(4-sulfamoylp... -

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Basic information

Entry
Database: PDB / ID: 7r1x
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-carbothioamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / sulfonamide / human carbonic anhydrase II / inhibitor / metalloenzyme
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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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 / one-carbon metabolic process / 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-HFF / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 3, 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

Downloads & links

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Assembly

Deposited unit
AAA: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8914
Polymers29,2891
Non-polymers6023
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-7 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.490, 41.680, 72.080
Angle α, β, γ (deg.)90.000, 104.513, 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-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.: 1 / Source method: obtained synthetically / Formula: C21H24N4O3S2 / 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.: 229 / 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: 41.7 %
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: Jun 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.35→41.17 Å / Num. obs: 53135 / % possible obs: 97.8 % / Redundancy: 5.83 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.054 / Net I/σ(I): 18.6
Reflection shellResolution: 1.35→1.38 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.19 / Num. unique obs: 3257 / CC1/2: 0.721 / Rrim(I) all: 0.663 / % possible all: 81.6

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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: 1.35→41.17 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.797 / SU ML: 0.033 / Cross valid method: NONE / ESU R: 0.051 / ESU R Free: 0.052
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1763 2592 4.878 %
Rwork0.1572 50543 -
all0.158 --
obs-53135 97.894 %
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: 16.188 Å2
Baniso -1Baniso -2Baniso -3
1--0.276 Å20 Å20.08 Å2
2--0.045 Å20 Å2
3---0.167 Å2
Refinement stepCycle: LAST / Resolution: 1.35→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 37 229 2320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132162
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161987
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.6332937
X-RAY DIFFRACTIONr_angle_other_deg1.4651.6044607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1445258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35423.645107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20115350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.608157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022516
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
X-RAY DIFFRACTIONr_nbd_refined0.2430.2405
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21899
X-RAY DIFFRACTIONr_nbtor_refined0.180.21012
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21008
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1990.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2750.216
X-RAY DIFFRACTIONr_nbd_other0.250.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.223
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_mcbond_it1.6711.4551034
X-RAY DIFFRACTIONr_mcbond_other1.6611.4481031
X-RAY DIFFRACTIONr_mcangle_it2.5222.1821288
X-RAY DIFFRACTIONr_mcangle_other2.522.1821288
X-RAY DIFFRACTIONr_scbond_it2.9561.751128
X-RAY DIFFRACTIONr_scbond_other2.9551.7491129
X-RAY DIFFRACTIONr_scangle_it4.382.5021648
X-RAY DIFFRACTIONr_scangle_other4.3792.5021649
X-RAY DIFFRACTIONr_lrange_it5.39718.1032392
X-RAY DIFFRACTIONr_lrange_other5.29217.6692347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3820.2551780.2553077X-RAY DIFFRACTION81.5994
1.382-1.4190.2151500.2153441X-RAY DIFFRACTION92.1715
1.419-1.4610.1951710.1863557X-RAY DIFFRACTION99.1226
1.461-1.5060.1941910.1713478X-RAY DIFFRACTION99.9455
1.506-1.5550.181310.163437X-RAY DIFFRACTION100
1.555-1.6090.1811480.1453308X-RAY DIFFRACTION99.654
1.609-1.670.1691850.1513137X-RAY DIFFRACTION99.9699
1.67-1.7380.171790.1463013X-RAY DIFFRACTION99.9374
1.738-1.8160.1761460.1472932X-RAY DIFFRACTION99.9675
1.816-1.9040.1841470.1532781X-RAY DIFFRACTION99.7275
1.904-2.0070.1841620.152651X-RAY DIFFRACTION99.858
2.007-2.1290.1841170.152546X-RAY DIFFRACTION99.7752
2.129-2.2750.1751510.1532313X-RAY DIFFRACTION99.9189
2.275-2.4580.1761070.1472233X-RAY DIFFRACTION99.9146
2.458-2.6920.169910.1562058X-RAY DIFFRACTION99.8606
2.692-3.0090.151840.1511856X-RAY DIFFRACTION99.9485
3.009-3.4730.1641050.1551619X-RAY DIFFRACTION99.7108
3.473-4.2510.177640.1441412X-RAY DIFFRACTION99.5951
4.251-6.0010.161470.1581085X-RAY DIFFRACTION99.2982
6.001-41.170.184380.182609X-RAY DIFFRACTION98.7786

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