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- PDB-9gfw: HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH 4-methylphenyl-boroni... -

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Basic information

Entry
Database: PDB / ID: 9gfw
TitleHUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH 4-methylphenyl-boronic acid at pH 7.4
ComponentsCarbonic anhydrase 2
KeywordsLYASE / CARBONIC ANHYDRASE II / PROTEIN-INHIBITOR COMPLEX / INHIBITOR / BORONIC ACID
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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / 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
: / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.07 Å
AuthorsAlterio, V. / De Simone, G. / Esposito, D.
Funding support Italy, 2items
OrganizationGrant numberCountry
Italian National Research Council (CNR)Joint Bilateral Agreements CNR/CINVESTAV Italy
Ministero dell Universita e della RicercaP2022EPH87 Italy
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Exploring the binding mode of phenyl and vinyl boronic acids to human carbonic anhydrases.
Authors: Esposito, D. / Monti, S.M. / Supuran, C.T. / Winum, J.Y. / De Simone, G. / Alterio, V.
History
DepositionAug 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9996
Polymers29,2891
Non-polymers7105
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-10 kcal/mol
Surface area11820 Å2
Unit cell
Length a, b, c (Å)42.195, 41.443, 72.084
Angle α, β, γ (deg.)90.00, 104.43, 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) / Tissue: ERYTHROCYTES / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 6 types, 214 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1IKU / (4-methylphenyl)-tris(oxidanyl)boron


Mass: 152.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10BO3 / 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: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: AMMONIUM SULPHATE 2.8 M, TRIS-HCL 50 MM, 4-HYDROXYMERCURYBENZOATE

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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: Apr 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.07→50 Å / Num. obs: 103340 / % possible obs: 97.1 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Net I/σ(I): 17.8
Reflection shellResolution: 1.07→1.09 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4889 / CC1/2: 0.916 / Rpim(I) all: 0.199 / Rrim(I) all: 0.422 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data reduction
SCALEPACKdata scaling
Omodel building
REFMAC5.8.0425phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.07→40.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.712 / SU ML: 0.017 / 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
Rfree0.16216 2125 2.1 %RANDOM
Rwork0.14145 ---
obs0.14187 101155 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0 Å2-0.42 Å2
2---0.02 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.07→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 32 209 2299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0420.0122208
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162021
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.8282998
X-RAY DIFFRACTIONr_angle_other_deg0.6761.7814686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9825269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.14257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.55910359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
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_it3.2490.9351061
X-RAY DIFFRACTIONr_mcbond_other3.2240.9341061
X-RAY DIFFRACTIONr_mcangle_it4.7461.6861335
X-RAY DIFFRACTIONr_mcangle_other4.7531.6881336
X-RAY DIFFRACTIONr_scbond_it4.8131.1471147
X-RAY DIFFRACTIONr_scbond_other4.8111.1481146
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8991.9891664
X-RAY DIFFRACTIONr_long_range_B_refined8.83911.22395
X-RAY DIFFRACTIONr_long_range_B_other8.50510.532356
X-RAY DIFFRACTIONr_rigid_bond_restr4.32434229
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.07→1.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 143 -
Rwork0.179 7130 -
obs--92.63 %

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