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- PDB-6gm9: Human Carbonic Anhydrase II in complex with 4-Methylbenzenesulfonamide -

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Basic information

Entry
Database: PDB / ID: 6gm9
TitleHuman Carbonic Anhydrase II in complex with 4-Methylbenzenesulfonamide
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 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
4-methylbenzenesulfonamide / beta-D-glucopyranose / alpha-D-glucopyranose / : / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.089 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
DepositionMay 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 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_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 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)31,2779
Polymers29,8071
Non-polymers1,4718
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-28 kcal/mol
Surface area11390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.365, 41.472, 72.273
Angle α, β, γ (deg.)90.00, 104.66, 90.00
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: 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

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Sugars , 2 types, 3 molecules

#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
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
#7: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


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

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Non-polymers , 5 types, 293 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.: 1 / Source method: obtained synthetically / Formula: Hg
#5: Chemical ChemComp-4J8 / 4-methylbenzenesulfonamide


Mass: 171.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9NO2S
#6: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 40.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammoniumsulfate 2.70 M, pH = 7.8, saturated with p-Chloromercurybenzoic 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: 1.089→41.472 Å / Num. obs: 99517 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.62 % / CC1/2: 0.998 / Rsym value: 0.045 / Net I/σ(I): 15.44
Reflection shellResolution: 1.089→1.095 Å / Redundancy: 3.64 % / Mean I/σ(I) obs: 5.15 / Num. unique obs: 15508 / CC1/2: 0.956 / Rsym value: 0.2377 / % possible all: 95.6

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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: 1.089→23.792 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 8.09
RfactorNum. reflection% reflectionSelection details
Rfree0.1184 4975 5 %Random selection of 5 % of reflections
Rwork0.1032 ---
obs0.104 99509 98.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.089→23.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 70 288 2377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082405
X-RAY DIFFRACTIONf_angle_d1.1253308
X-RAY DIFFRACTIONf_dihedral_angle_d13.239902
X-RAY DIFFRACTIONf_chiral_restr0.094348
X-RAY DIFFRACTIONf_plane_restr0.009454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0894-1.10180.12011520.1112889X-RAY DIFFRACTION91
1.1018-1.11480.12311610.10483059X-RAY DIFFRACTION94
1.1148-1.12840.11131570.09662993X-RAY DIFFRACTION96
1.1284-1.14270.10481640.09423118X-RAY DIFFRACTION97
1.1427-1.15770.10371650.09163121X-RAY DIFFRACTION98
1.1577-1.17360.11811650.08973135X-RAY DIFFRACTION98
1.1736-1.19030.12181640.08983117X-RAY DIFFRACTION98
1.1903-1.20810.10721680.09093188X-RAY DIFFRACTION98
1.2081-1.2270.1031630.08943100X-RAY DIFFRACTION98
1.227-1.24710.10681670.08773176X-RAY DIFFRACTION99
1.2471-1.26860.10631640.08583126X-RAY DIFFRACTION99
1.2686-1.29170.11411680.08753193X-RAY DIFFRACTION98
1.2917-1.31650.10971640.07973108X-RAY DIFFRACTION99
1.3165-1.34340.1061680.08063194X-RAY DIFFRACTION99
1.3434-1.37260.10351680.08253181X-RAY DIFFRACTION99
1.3726-1.40450.09641650.08283145X-RAY DIFFRACTION99
1.4045-1.43960.111680.08523190X-RAY DIFFRACTION99
1.4396-1.47850.09981690.08093215X-RAY DIFFRACTION99
1.4785-1.5220.0861660.083154X-RAY DIFFRACTION99
1.522-1.57120.1141680.08123197X-RAY DIFFRACTION99
1.5712-1.62730.10011660.08833138X-RAY DIFFRACTION99
1.6273-1.69240.10541690.093212X-RAY DIFFRACTION99
1.6924-1.76940.09811660.09343153X-RAY DIFFRACTION99
1.7694-1.86270.10011670.0943177X-RAY DIFFRACTION99
1.8627-1.97930.12931690.10013213X-RAY DIFFRACTION99
1.9793-2.13210.10841660.10513158X-RAY DIFFRACTION98
2.1321-2.34650.11751670.11323173X-RAY DIFFRACTION98
2.3465-2.68560.13331680.12233189X-RAY DIFFRACTION98
2.6856-3.3820.15781680.13133201X-RAY DIFFRACTION99
3.382-23.79780.1321750.12373321X-RAY DIFFRACTION99

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