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- PDB-8rou: Human Carbonic Anhydrase II in complex with biguanide derivative ... -

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Basic information

Entry
Database: PDB / ID: 8rou
TitleHuman Carbonic Anhydrase II in complex with biguanide derivative inhibitor 1-carbamimidamido-N-[(4 sulfamoylphenyl)methyl]methanimidamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / metalloenzyme / 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 / 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-PE3 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.08 Å
AuthorsBaroni, C. / Ferraroni, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)European Union
CitationJournal: To Be Published
Title: Human Carbonic Anhydrase II in complex with biguanide derivative inhibitor 1-carbamimidamido-N-[(4 sulfamoylphenyl)methyl]methanimidamide
Authors: Baroni, C. / Ferraroni, M.
History
DepositionJan 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4985
Polymers29,2891
Non-polymers1,2094
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-3 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.280, 41.090, 72.290
Angle α, β, γ (deg.)90.00, 104.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 277 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1H15 / 1-carbamimidoyl-3-[(4-sulfamoylphenyl)methyl]guanidine


Mass: 270.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N6O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 1.5 M sodium citrate, 50 mM Tris-HCl (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: 1.0001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.08→70.08 Å / Num. obs: 102568 / % possible obs: 99.8 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.089 / Net I/σ(I): 9.8
Reflection shellResolution: 1.08→1.1 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.403 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5042 / CC1/2: 0.341 / Rrim(I) all: 1.591 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XSCALEdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.08→70.08 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.962 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15151 5023 4.9 %RANDOM
Rwork0.13014 ---
obs0.13118 97452 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.356 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.14 Å2
2---0.06 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.08→70.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 54 273 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122280
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162035
X-RAY DIFFRACTIONr_angle_refined_deg1.91.6593120
X-RAY DIFFRACTIONr_angle_other_deg0.7491.5914725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8495290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.518511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59310320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022765
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02521
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8341.2461115
X-RAY DIFFRACTIONr_mcbond_other3.7981.2451115
X-RAY DIFFRACTIONr_mcangle_it5.382.2421420
X-RAY DIFFRACTIONr_mcangle_other5.3892.2441421
X-RAY DIFFRACTIONr_scbond_it5.3651.4421165
X-RAY DIFFRACTIONr_scbond_other5.3641.4431166
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4742.5331701
X-RAY DIFFRACTIONr_long_range_B_refined10.2616.912551
X-RAY DIFFRACTIONr_long_range_B_other10.09416.632542
X-RAY DIFFRACTIONr_rigid_bond_restr3.88134315
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.081→1.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 362 -
Rwork0.3 7109 -
obs--98.68 %

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