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- PDB-3s8x: Crystal structure of human carbonic anhydrase isozyme II with 4-{... -

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Basic information

Entry
Database: PDB / ID: 3s8x
TitleCrystal structure of human carbonic anhydrase isozyme II with 4-{[(4-methyl-6-oxo-1,6-dihydro-2-pyrimidinyl)sulfanyl]acetyl}benzenesulfonamide
ComponentsCarbonic anhydrase 2
Keywordslyase/lyase inhibitor / drug design / carbonic anhydrase / sulfonamide / metal-binding / 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
Chem-E59 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.3 Å
AuthorsGrazulis, S. / Manakova, E. / Tamulaitiene, G.
CitationJournal: Eur.J.Med.Chem. / Year: 2012
Title: Design of [(2-pyrimidinylthio)acetyl]benzenesulfonamides as inhibitors of human carbonic anhydrases.
Authors: Capkauskaite, E. / Zubriene, A. / Baranauskiene, L. / Tamulaitiene, G. / Manakova, E. / Kairys, V. / Grazulis, S. / Tumkevicius, S. / Matulis, D.
History
DepositionMay 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0136
Polymers29,2891
Non-polymers7245
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.208, 41.180, 71.918
Angle α, β, γ (deg.)90.000, 104.290, 90.000
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 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 253 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical ChemComp-E59 / 4-{[(4-methyl-6-oxo-1,6-dihydropyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide


Mass: 339.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13N3O4S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.07 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 9
Details: Na-Bicine 0.1M pH 9, Na-Malonate 2.2M pH 7, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9748 Å
DetectorType: MARMosaic, 225 mm / Detector: CCD / Date: Nov 14, 2010 / Details: Detector swing-out angle up to 30 degrees
RadiationMonochromator: Double crystal Si(111), horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9748 Å / Relative weight: 1
ReflectionResolution: 1.3→41.18 Å / Num. obs: 56499 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 12.15 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 26.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.3-1.377.70.3826215880220.3893.6
1.37-1.457.70.2662.85921876420.26694.3
1.45-1.557.80.1784.25576071920.17894.8
1.55-1.687.70.1275.75247667810.12795.6
1.68-1.847.70.0927.64882063220.09296.3
1.84-2.067.70.0699.54402557430.06996.9
2.06-2.377.60.0610.73859950880.0697.5
2.37-2.917.50.05511.33273543670.05598.2
2.91-4.117.30.04812.12490534180.04898.7
4.11-41.186.90.046121329219240.04698.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
SCALA3.2.19data scaling
PDB_EXTRACT3.006data extraction
MAR345v. 0.10.22 on RedHat Linux 8data collection
RefinementMethod to determine structure: molecular replacement
Starting model: 3HLJ

3hlj


Resolution: 1.3→39.84 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.141 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.903 / SU R Cruickshank DPI: 0.057 / SU Rfree: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.179 5694 10.1 %RANDOM
Rwork0.142 ---
obs0.146 56478 95.53 %-
all-56499 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.13 Å2 / Biso mean: 16.21 Å2 / Biso min: 6.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--0.54 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 42 248 2339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222261
X-RAY DIFFRACTIONr_angle_refined_deg2.3481.9763081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6065275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15924.951103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96815370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.139157
X-RAY DIFFRACTIONr_chiral_restr0.1910.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021769
X-RAY DIFFRACTIONr_nbd_refined0.2260.21064
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21517
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2208
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.241
X-RAY DIFFRACTIONr_mcbond_it2.9281.51341
X-RAY DIFFRACTIONr_mcangle_it3.83622178
X-RAY DIFFRACTIONr_scbond_it4.9923920
X-RAY DIFFRACTIONr_scangle_it6.2844.5903
X-RAY DIFFRACTIONr_rigid_bond_restr3.30532261
X-RAY DIFFRACTIONr_sphericity_free15.5813249
X-RAY DIFFRACTIONr_sphericity_bonded9.39132192
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 398 -
Rwork0.217 3642 -
all-4040 -
obs--92.89 %

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