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

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Basic information

Entry
Database: PDB / ID: 8row
TitleHuman Carbonic Anhydrase II in complex with biguanide derivative inhibitor 1-carbamimidamido-N-[(4 sulfamoylphenyl)methyl]methanimidamide, using glycerol as cryoprotectant
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
: / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsBaroni, C. / Ferraroni, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)B83C22003920001European Union
CitationJournal: To Be Published
Title: Human Carbonic Anhydrase II in complex with biguanide derivative inhibitor 1-carbamimidamido-N-[(4 sulfamoylphenyl)methyl]methanimidamide, using glycerol as cryoprotectant
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)29,9875
Polymers29,2891
Non-polymers6984
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-7 kcal/mol
Surface area11210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.440, 41.300, 72.030
Angle α, β, γ (deg.)90.00, 104.29, 90.00
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-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.: 2 / Source method: obtained synthetically / Formula: C9H14N6O2S / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
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: 0.9718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.05→40.015 Å / Num. obs: 107024 / % possible obs: 95 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.054 / Net I/σ(I): 16.7
Reflection shellResolution: 1.05→1.068 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4661 / CC1/2: 0.715 / Rrim(I) all: 0.801 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XSCALEdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.05→40.015 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.615 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13856 5295 4.9 %RANDOM
Rwork0.11603 ---
obs0.11711 101727 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.483 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20.01 Å2
2---0.07 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.05→40.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 39 254 2298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122268
X-RAY DIFFRACTIONr_bond_other_d0.0040.0162047
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.6643110
X-RAY DIFFRACTIONr_angle_other_deg0.7181.64730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1525283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.015514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6810325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022731
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02534
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_it3.9211.1161091
X-RAY DIFFRACTIONr_mcbond_other3.91.1161091
X-RAY DIFFRACTIONr_mcangle_it5.6612.0121380
X-RAY DIFFRACTIONr_mcangle_other5.6642.0141381
X-RAY DIFFRACTIONr_scbond_it5.8431.3121177
X-RAY DIFFRACTIONr_scbond_other5.8411.3121178
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8962.3081728
X-RAY DIFFRACTIONr_long_range_B_refined10.71116.572498
X-RAY DIFFRACTIONr_long_range_B_other10.27614.532443
X-RAY DIFFRACTIONr_rigid_bond_restr4.36334315
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 347 -
Rwork0.221 6717 -
obs--84.78 %

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