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- PDB-3sbi: Crystal structure of human carbonic anhydrase isozyme II with 4-[... -

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Basic information

Entry
Database: PDB / ID: 3sbi
TitleCrystal structure of human carbonic anhydrase isozyme II with 4-[(2-pyrimidinylsulfanyl)acetyl]benzenesulfonamide
ComponentsCarbonic anhydrase 2
Keywordslyase/lyase inhibitor / drug design / 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 / 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 / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
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-E90 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.4 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
DepositionJun 5, 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 15, 2017Group: Advisory / Database references
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_database_related.db_name
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9836
Polymers29,2891
Non-polymers6945
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.348, 41.314, 72.240
Angle α, β, γ (deg.)90.000, 104.250, 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, 325 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-E90 / 4-[(pyrimidin-2-ylsulfanyl)acetyl]benzenesulfonamide


Mass: 309.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11N3O3S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 41.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 0.1M Na-bicine pH 9, 2M Na-malonate pH 7.55, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 12, 2010 / Details: Bent, vertically focussing mirrors
RadiationMonochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.4→20.68 Å / Num. obs: 46467 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 25.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.4860.34424033266750.34495.7
1.48-1.5760.2363.13792363040.23695.9
1.57-1.6760.1644.43572759410.16496.7
1.67-1.8160.1116.63374956140.11197.1
1.81-1.9860.06810.73100051640.06897.4
1.98-2.2160.04316.42800946780.04397.7
2.21-2.5660.03321.52497241890.03398.3
2.56-3.135.90.02526.72116135610.02598.6
3.13-4.435.90.01832.91632427840.01899
4.43-20.685.60.01831.5874415570.01898.1

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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
DNAdata collection
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 3HLJ

3hlj


Resolution: 1.4→20.66 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.132 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.913 / SU R Cruickshank DPI: 0.072 / SU Rfree: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.183 4705 10.1 %RANDOM
Rwork0.133 ---
all0.138 46451 --
obs0.138 46451 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.52 Å2 / Biso mean: 14.597 Å2 / Biso min: 4.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0.05 Å2
2---0.19 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 40 320 2419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0212308
X-RAY DIFFRACTIONr_angle_refined_deg2.2341.963148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7955287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90824.86107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76715379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.742157
X-RAY DIFFRACTIONr_chiral_restr0.1820.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021818
X-RAY DIFFRACTIONr_nbd_refined0.2340.21061
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2233
X-RAY DIFFRACTIONr_metal_ion_refined0.0340.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.263
X-RAY DIFFRACTIONr_mcbond_it2.7211.51384
X-RAY DIFFRACTIONr_mcangle_it3.63722252
X-RAY DIFFRACTIONr_scbond_it4.6623924
X-RAY DIFFRACTIONr_scangle_it5.9244.5896
X-RAY DIFFRACTIONr_rigid_bond_restr3.06532308
X-RAY DIFFRACTIONr_sphericity_free13.6993321
X-RAY DIFFRACTIONr_sphericity_bonded7.85332233
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 316 -
Rwork0.18 3028 -
all-3344 -
obs-3028 95.38 %

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