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- PDB-7qse: human Carbonic Anhydrase II in complex with N-(2-aminophenyl)-4-(... -

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Basic information

Entry
Database: PDB / ID: 7qse
Titlehuman Carbonic Anhydrase II in complex with N-(2-aminophenyl)-4-((2-oxo-2-((4-sulfamoylbenzyl)amino)ethyl)amino)benzamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase / metalloenzyme / sulfonamide / inhibitor
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 / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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-EUM / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.428 Å
AuthorsAngeli, A. / Ferraroni, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: human Carbonic Anhydrase II in complex with N-(2-aminophenyl)-4-((2-oxo-2-((4-sulfamoylbenzyl)amino)ethyl)amino)benzamide
Authors: Angeli, A. / Ferraroni, M.
History
DepositionJan 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / struct
Item: _citation.title / _struct.title
Revision 1.2Jan 31, 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)29,9004
Polymers29,2891
Non-polymers6113
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-9 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.317, 41.243, 72.085
Angle α, β, γ (deg.)90.000, 104.346, 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EUM / ~{N}-(2-aminophenyl)-4-[[2-oxidanylidene-2-[(4-sulfamoylphenyl)methylamino]ethyl]amino]benzamide / N-(2-aminophenyl)-4-((2-oxo-2-((4-sulfamoylbenzyl)amino)ethyl)amino)benzamide


Mass: 453.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23N5O4S / 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 293 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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.428→41.24 Å / Num. obs: 43568 / % possible obs: 97.2 % / Redundancy: 6.4 % / CC1/2: 1 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.019 / Rrim(I) all: 0.035 / Net I/σ(I): 32.9
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.261 / Num. unique obs: 2006 / CC1/2: 0.93 / Rpim(I) all: 0.184 / Rrim(I) all: 0.321 / % possible all: 92.4

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Processing

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

4fik


Resolution: 1.428→35.538 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.802 / SU ML: 0.032 / Cross valid method: NONE / ESU R: 0.058 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1642 2236 5.135 %
Rwork0.147 41312 -
all0.148 --
obs-43548 96.905 %
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: 14.597 Å2
Baniso -1Baniso -2Baniso -3
1--0.115 Å2-0 Å2-0.108 Å2
2--0.017 Å20 Å2
3---0.135 Å2
Refinement stepCycle: LAST / Resolution: 1.428→35.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 39 221 2314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132174
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162002
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.6332951
X-RAY DIFFRACTIONr_angle_other_deg1.4921.6014637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2375260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54123.645107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73715352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.318157
X-RAY DIFFRACTIONr_chiral_restr0.1050.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022558
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02492
X-RAY DIFFRACTIONr_nbd_refined0.2350.2412
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21933
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21028
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21003
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2132
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2890.217
X-RAY DIFFRACTIONr_nbd_other0.2490.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.219
X-RAY DIFFRACTIONr_mcbond_it1.491.281035
X-RAY DIFFRACTIONr_mcbond_other1.491.2821036
X-RAY DIFFRACTIONr_mcangle_it2.1911.9211290
X-RAY DIFFRACTIONr_mcangle_other2.191.9241291
X-RAY DIFFRACTIONr_scbond_it2.7681.5921139
X-RAY DIFFRACTIONr_scbond_other2.7671.5911140
X-RAY DIFFRACTIONr_scangle_it4.22.2651659
X-RAY DIFFRACTIONr_scangle_other4.1992.2651660
X-RAY DIFFRACTIONr_lrange_it5.0916.2122402
X-RAY DIFFRACTIONr_lrange_other4.97115.8262360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.428-1.4650.2091690.1882921X-RAY DIFFRACTION93.5797
1.465-1.5060.2081450.1592927X-RAY DIFFRACTION95.7308
1.506-1.5490.1921740.1562818X-RAY DIFFRACTION96.144
1.549-1.5970.1761640.1432784X-RAY DIFFRACTION95.9635
1.597-1.6490.21480.1422672X-RAY DIFFRACTION96.1145
1.649-1.7070.1911390.1482608X-RAY DIFFRACTION96.5214
1.707-1.7710.1711340.1422540X-RAY DIFFRACTION96.8139
1.771-1.8440.1651490.1422411X-RAY DIFFRACTION95.6294
1.844-1.9260.1511320.1462326X-RAY DIFFRACTION97.1926
1.926-2.020.1741180.1432266X-RAY DIFFRACTION97.7049
2.02-2.1290.1711230.1482132X-RAY DIFFRACTION97.8308
2.129-2.2580.1721020.1452062X-RAY DIFFRACTION98.0517
2.258-2.4130.156930.1381930X-RAY DIFFRACTION98.3471
2.413-2.6070.1541150.151780X-RAY DIFFRACTION98.5439
2.607-2.8550.183830.1511678X-RAY DIFFRACTION98.545
2.855-3.1910.166830.1531514X-RAY DIFFRACTION98.7631
3.191-3.6840.151540.1351360X-RAY DIFFRACTION99.0196
3.684-4.5080.128450.1231170X-RAY DIFFRACTION99.1028
4.508-6.3630.114490.114881X-RAY DIFFRACTION98.831
6.363-35.5380.208170.189532X-RAY DIFFRACTION98.5637

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