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- PDB-6hqx: Human Carbonic Anhydrase II in complex with 4-Ethylbenzenesulfonamide -

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Basic information

Entry
Database: PDB / ID: 6hqx
TitleHuman Carbonic Anhydrase II in complex with 4-Ethylbenzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inhibitor / Complex / CO2-conversion
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 / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
4-ethylbenzenesulfonamide / (4-CARBOXYPHENYL)(CHLORO)MERCURY / beta-D-glucopyranose / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.097 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Conformational Changes in Alkyl Chains Determine the Thermodynamic and Kinetic Binding Profiles of Carbonic Anhydrase Inhibitors.
Authors: Glockner, S. / Ngo, K. / Sager, C.P. / Hufner-Wulsdorf, T. / Heine, A. / Klebe, G.
History
DepositionSep 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)30,9807
Polymers29,8071
Non-polymers1,1746
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-28 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.305, 41.424, 72.222
Angle α, β, γ (deg.)90.00, 104.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 29806.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first five amino acids (GSPEF) of the sample sequence are remnants of an expression tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: P00918, carbonic anhydrase
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 279 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2
#5: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#6: Chemical ChemComp-4JC / 4-ethylbenzenesulfonamide


Mass: 185.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulfate 2.70 M, pH = 7.8, saturated with p-Chloromercuribenzoic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 3, 2017 / Details: Sagitally bended Si(111) crystal
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.097→41.424 Å / Num. obs: 97587 / % possible obs: 98.6 % / Redundancy: 3.61 % / CC1/2: 0.999 / Rsym value: 0.052 / Net I/σ(I): 12.54
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 3.56 % / Mean I/σ(I) obs: 2.86 / Num. unique obs: 15119 / CC1/2: 0.891 / Rsym value: 0.339 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.097→23.748 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.39
RfactorNum. reflection% reflectionSelection details
Rfree0.1389 4879 5 %Random selection 5 %
Rwork0.1218 ---
obs0.1227 97575 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.097→23.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 47 274 2329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082348
X-RAY DIFFRACTIONf_angle_d1.0723225
X-RAY DIFFRACTIONf_dihedral_angle_d13.595873
X-RAY DIFFRACTIONf_chiral_restr0.089335
X-RAY DIFFRACTIONf_plane_restr0.008447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0974-1.10990.1531330.182517X-RAY DIFFRACTION81
1.1099-1.1230.18891600.15683045X-RAY DIFFRACTION98
1.123-1.13660.19261600.15253038X-RAY DIFFRACTION99
1.1366-1.1510.15221630.15193100X-RAY DIFFRACTION99
1.151-1.16620.18961630.14693106X-RAY DIFFRACTION100
1.1662-1.18220.16761660.14023138X-RAY DIFFRACTION100
1.1822-1.1990.14941600.13973039X-RAY DIFFRACTION100
1.199-1.21690.15271650.13383138X-RAY DIFFRACTION100
1.2169-1.2360.15781640.13113120X-RAY DIFFRACTION99
1.236-1.25620.13951640.12163114X-RAY DIFFRACTION100
1.2562-1.27790.13791620.12183079X-RAY DIFFRACTION100
1.2779-1.30110.14391630.11363104X-RAY DIFFRACTION100
1.3011-1.32610.14371660.10853155X-RAY DIFFRACTION100
1.3261-1.35320.12761620.11033068X-RAY DIFFRACTION100
1.3532-1.38260.11831650.1083139X-RAY DIFFRACTION100
1.3826-1.41480.12281630.10433103X-RAY DIFFRACTION100
1.4148-1.45020.13021650.10463126X-RAY DIFFRACTION100
1.4502-1.48940.13371630.10073093X-RAY DIFFRACTION100
1.4894-1.53320.12021640.09883121X-RAY DIFFRACTION100
1.5332-1.58270.11381620.10033073X-RAY DIFFRACTION99
1.5827-1.63920.13081640.10163123X-RAY DIFFRACTION99
1.6392-1.70480.15411640.10863109X-RAY DIFFRACTION99
1.7048-1.78240.12091630.10923098X-RAY DIFFRACTION99
1.7824-1.87630.12941640.10953113X-RAY DIFFRACTION99
1.8763-1.99380.14131640.1143122X-RAY DIFFRACTION99
1.9938-2.14770.1361630.11623098X-RAY DIFFRACTION99
2.1477-2.36360.13041640.12283116X-RAY DIFFRACTION99
2.3636-2.70520.13391650.13053126X-RAY DIFFRACTION99
2.7052-3.40670.15761650.13783142X-RAY DIFFRACTION99
3.4067-23.75320.13411700.12673233X-RAY DIFFRACTION99

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