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- PDB-5doh: Crystal structure of human carbonic anhydrase isozyme II with 2-[... -

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Basic information

Entry
Database: PDB / ID: 5doh
TitleCrystal structure of human carbonic anhydrase isozyme II with 2-[(1S)-2,3-Dihydro-1H-inden-1-ylamino]-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / 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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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-5DU / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.05 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: ChemMedChem / Year: 2017
Title: Intrinsic Thermodynamics and Structures of 2,4- and 3,4-Substituted Fluorinated Benzenesulfonamides Binding to Carbonic Anhydrases.
Authors: Zubriene, A. / Smirnov, A. / Dudutiene, V. / Timm, D.D. / Matuliene, J. / Michailoviene, V. / Zaksauskas, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionSep 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Aug 21, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,02810
Polymers58,5782
Non-polymers1,4508
Water9,692538
1
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0145
Polymers29,2891
Non-polymers7254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0145
Polymers29,2891
Non-polymers7254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.162, 41.157, 71.854
Angle α, β, γ (deg.)90.000, 104.190, 90.000
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carbonic anhydrase 2 / / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 2 / Fragment: human carbonic anhydrase II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 546 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Fragment: 2-[(1S)-2,3-Dihydro-1H-inden-1-ylamino]-3,5,6-trifluoro-4-[(2-hy-droxyethyl)thio]benzenesulfonamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 2 / Fragment: Zn / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Fragment: BICINE / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-5DU / 2-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-3,5,6-trifluoro-4-[(2-hydroxyethyl)sulfanyl]benzenesulfonamide


Mass: 418.454 Da / Num. of mol.: 2 / Fragment: DIMETHYL SULFOXIDE / Source method: obtained synthetically / Formula: C17H17F3N2O3S2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.01 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallization buffer: 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

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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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.05→69.661 Å / Num. all: 195453 / Num. obs: 195453 / % possible obs: 89.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 8.491 Å2 / Rpim(I) all: 0.023 / Rrim(I) all: 0.044 / Rsym value: 0.031 / Net I/av σ(I): 8.754 / Net I/σ(I): 17.1 / Num. measured all: 735878
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.05-1.113.70.3790.2712.9103595277500.190.380.27113.786.7
1.11-1.173.80.2270.1584.899829264920.120.230.1586.287.5
1.17-1.253.80.1670.1156.695998252910.090.170.1158.389.2
1.25-1.363.70.1240.084986473231000.060.120.0841187.5
1.36-1.483.80.0880.05912.685035221780.050.090.05915.491.3
1.48-1.663.70.0630.0417.672675194830.030.060.0421.488.5
1.66-1.923.80.0460.0321.969794181640.020.050.0329.493.5
1.92-2.353.70.0380.02524.953832146090.020.040.02536.889.2
2.35-3.323.80.0340.02423.845216119670.020.030.0244294.7
3.32-69.663.70.0330.024232343164190.020.030.02444.692.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.006data extraction
REFMAC5.6.0117refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLJ

3hlj


Resolution: 1.05→69.66 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.179 / WRfactor Rwork: 0.148 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.917 / SU R Cruickshank DPI: 0.032 / SU Rfree: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.172 19404 9.9 %RANDOM
Rwork0.144 176047 --
obs0.147 195451 89.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 138.81 Å2 / Biso mean: 16.924 Å2 / Biso min: 6.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20.04 Å20.01 Å2
2---0.14 Å20.02 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.05→69.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4118 0 86 538 4742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.024564
X-RAY DIFFRACTIONr_angle_refined_deg2.3071.9666232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35624.66206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36715733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7171514
X-RAY DIFFRACTIONr_chiral_restr0.1480.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213588
X-RAY DIFFRACTIONr_rigid_bond_restr9.28634564
X-RAY DIFFRACTIONr_sphericity_free34.1785540
X-RAY DIFFRACTIONr_sphericity_bonded16.44154412
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 1417 -
Rwork0.212 12729 -
all-14146 -
obs--87.53 %

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