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- PDB-6i2f: Human Carbonic Anhydrase II in complex with 4-Propoxybenzenesulfo... -

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Basic information

Entry
Database: PDB / ID: 6i2f
TitleHuman Carbonic Anhydrase II in complex with 4-Propoxybenzenesulfonamide
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 / 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, 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-propoxybenzenesulfonamide / beta-D-glucopyranose / : / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.198 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
DepositionNov 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 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)30,9907
Polymers29,8071
Non-polymers1,1846
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-55 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.223, 41.398, 72.031
Angle α, β, γ (deg.)90.00, 104.39, 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 5 amino acids (GSPEF) 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
#5: 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, 283 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#6: Chemical ChemComp-3W6 / 4-propoxybenzenesulfonamide


Mass: 215.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO3S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammoniumsulfate 2.70 M, pH = 7.8, saturated with para-Chloromercuribenzoic acid.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 4, 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: 1.19→41.398 Å / Num. obs: 72714 / % possible obs: 93.5 % / Redundancy: 3.84 % / Biso Wilson estimate: 9.483 Å2 / CC1/2: 0.999 / Rsym value: 0.042 / Net I/σ(I): 17.71
Reflection shellResolution: 1.19→1.26 Å / Redundancy: 3.74 % / Mean I/σ(I) obs: 6.34 / Num. unique obs: 11290 / CC1/2: 0.976 / Rsym value: 0.191 / % possible all: 90.1

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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: 1.198→23.784 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 11.17
RfactorNum. reflection% reflectionSelection details
Rfree0.1388 3549 5 %Random set of 5 %
Rwork0.1162 ---
obs0.1174 70978 93.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.198→23.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 39 278 2317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012349
X-RAY DIFFRACTIONf_angle_d1.1593225
X-RAY DIFFRACTIONf_dihedral_angle_d13.31868
X-RAY DIFFRACTIONf_chiral_restr0.09336
X-RAY DIFFRACTIONf_plane_restr0.008440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1983-1.21470.15191290.13022454X-RAY DIFFRACTION86
1.2147-1.2320.13561390.11112643X-RAY DIFFRACTION92
1.232-1.25040.13851390.09962643X-RAY DIFFRACTION92
1.2504-1.270.12311380.09722619X-RAY DIFFRACTION92
1.27-1.29080.14811410.09492676X-RAY DIFFRACTION92
1.2908-1.3130.13371390.09112632X-RAY DIFFRACTION93
1.313-1.33690.11011400.09432666X-RAY DIFFRACTION93
1.3369-1.36260.14091420.09452690X-RAY DIFFRACTION93
1.3626-1.39040.12821390.09312658X-RAY DIFFRACTION93
1.3904-1.42070.12271420.09082684X-RAY DIFFRACTION94
1.4207-1.45370.11391410.08872692X-RAY DIFFRACTION93
1.4537-1.490.13321410.09062669X-RAY DIFFRACTION94
1.49-1.53030.10551430.08612716X-RAY DIFFRACTION94
1.5303-1.57530.13631420.08882707X-RAY DIFFRACTION94
1.5753-1.62620.10851420.08952696X-RAY DIFFRACTION94
1.6262-1.68430.11191440.09432727X-RAY DIFFRACTION94
1.6843-1.75170.13311410.0982691X-RAY DIFFRACTION94
1.7517-1.83140.13531440.10482733X-RAY DIFFRACTION95
1.8314-1.92790.14661450.11022742X-RAY DIFFRACTION94
1.9279-2.04860.15341430.11182734X-RAY DIFFRACTION95
2.0486-2.20670.14111440.11882736X-RAY DIFFRACTION95
2.2067-2.42860.14161450.12512747X-RAY DIFFRACTION94
2.4286-2.77960.16181440.13592734X-RAY DIFFRACTION94
2.7796-3.50020.16121480.14482814X-RAY DIFFRACTION96
3.5002-23.78840.13051540.13482926X-RAY DIFFRACTION98

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