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- PDB-4q6e: Crystal structure of human carbonic anhydrase isozyme II with 4-{... -

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Basic information

Entry
Database: PDB / ID: 4q6e
TitleCrystal structure of human carbonic anhydrase isozyme II with 4-{[3-(3,5-Dimethyl-1H-pyrazol-1-yl)-3-oxopropyl]amino}benzene-1-sulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / benzenesulfonamide / 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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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-KR5 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.12 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Molecules / Year: 2014
Title: 4-Amino-substituted Benzenesulfonamides as Inhibitors of Human Carbonic Anhydrases.
Authors: Rutkauskas, K. / Zubriene, A. / Tumosiene, I. / Kantminiene, K. / Kazemekaite, M. / Smirnov, A. / Kazokaite, J. / Morkunaite, V. / Capkauskaite, E. / Manakova, E. / Grazulis, S. / ...Authors: Rutkauskas, K. / Zubriene, A. / Tumosiene, I. / Kantminiene, K. / Kazemekaite, M. / Smirnov, A. / Kazokaite, J. / Morkunaite, V. / Capkauskaite, E. / Manakova, E. / Grazulis, S. / Beresnevicius, Z.J. / Matulis, D.
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 20, 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 / 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 / _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)29,9966
Polymers29,2891
Non-polymers7075
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.237, 41.241, 72.189
Angle α, β, γ (deg.)90.000, 104.300, 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, 326 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-KR5 / 4-{[3-(3,5-dimethyl-1H-pyrazol-1-yl)-3-oxopropyl]amino}benzenesulfonamide


Mass: 322.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N4O3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.03 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.826606 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2014
RadiationMonochromator: High Heat Load (HHL) Monochromator: Si 111; Large Offset Monochromator (LOM) : Si 311, Si 511
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.12→41.241 Å / Num. obs: 85569 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 8.915 Å2 / Rsym value: 0.063 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.12-1.185.20.1933.64682789520.19366.7
1.18-1.255.90.1674.267542113890.16789.9
1.25-1.346.60.135.577973117790.1398.8
1.34-1.456.60.0957.572218109280.09598.5
1.45-1.596.70.0729.567407101160.07298.6
1.59-1.776.70.06210.76106890780.06297.9
1.77-2.056.90.05810.85614180980.05899
2.05-2.516.80.05711.54724269010.05799.2
2.51-3.556.90.058103700653330.05898.8
3.55-41.246.60.0618.21979829950.06198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.006data extraction
HKL-2000data collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 3HLJ

3hlj


Resolution: 1.12→39.88 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.168 / WRfactor Rwork: 0.134 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.936 / SU R Cruickshank DPI: 0.034 / SU Rfree: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.158 8572 10 %RANDOM
Rwork0.13 ---
all0.133 85523 --
obs0.133 85523 92.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 74.68 Å2 / Biso mean: 15.119 Å2 / Biso min: 5.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.12 Å2
2---0.19 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.12→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 42 321 2412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022309
X-RAY DIFFRACTIONr_angle_refined_deg2.3621.9683155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7655292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81524.37596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66315374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.828157
X-RAY DIFFRACTIONr_chiral_restr0.1770.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211799
X-RAY DIFFRACTIONr_rigid_bond_restr8.45732309
X-RAY DIFFRACTIONr_sphericity_free17.8345322
X-RAY DIFFRACTIONr_sphericity_bonded8.452230
LS refinement shellResolution: 1.121→1.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.165 348 -
Rwork0.132 3349 -
all-3697 -
obs--54.54 %

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