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- PDB-4kuy: Crystal structure of human carbonic anhydrase II in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4kuy
TitleCrystal structure of human carbonic anhydrase II in complex with the 5-(3-(o-tolylsulfonyl)ureido)pyridine-2-sulfonamide inhibitor
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE inhibitor / LYASE / LYASE-LYASE inhibitor complex
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 / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / cytoplasm / cytosol
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Chem-MB4 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsFerraroni, M.
CitationJournal: to be published
Title: New classes of carbonic anhydrase inhibitors
Authors: Ferraroni, M. / Supuran, C.T. / Carta, F. / Bozdag, M. / Scozzafava, A.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,5395
Polymers28,9331
Non-polymers6064
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.210, 41.186, 71.956
Angle α, β, γ (deg.)90.000, 104.190, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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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: 28932.641 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) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 365 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#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-MB4 / 5-({[(2-methylphenyl)sulfonyl]carbamoyl}amino)pyridine-2-sulfonamide


Mass: 370.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N4O5S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 8
Details: 1.5 M sodium citrate, Tris 50 mM, pH 8.0, vapor diffusion, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.542 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: May 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.65→29.029 Å / Num. obs: 28318 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.619 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 18.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.750.3622.228330403987.3
1.75-1.870.21549726429298.1
1.87-2.020.1257.610556406799.4
2.02-2.210.08713.1512768373499.9
2.21-2.470.06518.6713693342199.9
2.47-2.850.05227.0115235301299.9
2.85-3.480.03241.6813165257399.8
3.48-4.890.02257.1110142200399.8
4.890.02254.615817117799.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3P58

3p58


Resolution: 1.65→29.05 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.1727 / WRfactor Rwork: 0.141 / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.9019 / SU B: 1.792 / SU ML: 0.061 / SU R Cruickshank DPI: 0.1039 / SU Rfree: 0.0983 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 1440 5.1 %RANDOM
Rwork0.1574 ---
obs0.1589 28306 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 48.43 Å2 / Biso mean: 12.122 Å2 / Biso min: 3.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å20.01 Å2
2---0.15 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 35 361 2434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192256
X-RAY DIFFRACTIONr_bond_other_d0.0020.022117
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9683093
X-RAY DIFFRACTIONr_angle_other_deg0.71834925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65524.904104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58115381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.121157
X-RAY DIFFRACTIONr_chiral_restr0.0710.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
X-RAY DIFFRACTIONr_mcbond_it0.4930.9631069
X-RAY DIFFRACTIONr_mcbond_other0.4870.9611068
X-RAY DIFFRACTIONr_mcangle_it0.8851.4391344
LS refinement shellResolution: 1.652→1.695 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 80 -
Rwork0.246 1593 -
all-1673 -
obs--78.84 %

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