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- PDB-6gdc: Human Carbonic Anhydrase II in complex with Benzenesulfonamide -

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Basic information

Entry
Database: PDB / ID: 6gdc
TitleHuman Carbonic Anhydrase II in complex with Benzenesulfonamide
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 / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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
beta-D-glucopyranose / benzenesulfonamide / alpha-D-glucopyranose / : / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.079 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
DepositionApr 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 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)31,0698
Polymers29,8071
Non-polymers1,2627
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-30 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.320, 41.432, 72.163
Angle α, β, γ (deg.)90.00, 104.50, 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 5 amino acids (GSPEF) are remainders of and 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, 2 molecules

#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
#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, 252 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
#4: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#6: Chemical ChemComp-FB2 / benzenesulfonamide


Mass: 157.190 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 40.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.8
Details: Ammoniumsulfate 2.70 M, pH=7.8, saturated with para-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: 1.079→41.432 Å / Num. obs: 102486 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 9.127 Å2 / CC1/2: 0.999 / Rsym value: 0.042 / Net I/σ(I): 15.86
Reflection shellResolution: 1.079→1.084 Å / Redundancy: 3.53 % / Mean I/σ(I) obs: 5.09 / Num. unique obs: 15973 / CC1/2: 0.996 / Rsym value: 0.178 / % 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: 1.079→23.288 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 9.22
Details: Phenix refinement against 5 % of Free R value test set selection
RfactorNum. reflection% reflectionSelection details
Rfree0.1301 5124 5 %Random selection of 5 % of reflections
Rwork0.1149 ---
obs0.1157 102474 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.079→23.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 56 247 2315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072388
X-RAY DIFFRACTIONf_angle_d1.0693282
X-RAY DIFFRACTIONf_dihedral_angle_d15.847894
X-RAY DIFFRACTIONf_chiral_restr0.088342
X-RAY DIFFRACTIONf_plane_restr0.008457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0787-1.0910.12851520.12412885X-RAY DIFFRACTION88
1.091-1.10380.1291630.11733092X-RAY DIFFRACTION95
1.1038-1.11730.11741680.10633203X-RAY DIFFRACTION96
1.1173-1.13140.11441690.10323206X-RAY DIFFRACTION99
1.1314-1.14630.10871720.09993259X-RAY DIFFRACTION98
1.1463-1.1620.11511710.09883262X-RAY DIFFRACTION100
1.162-1.17860.11911730.09513276X-RAY DIFFRACTION99
1.1786-1.19620.10591700.09433224X-RAY DIFFRACTION100
1.1962-1.21490.12161720.0953285X-RAY DIFFRACTION99
1.2149-1.23480.12441730.09453288X-RAY DIFFRACTION100
1.2348-1.25610.10621720.09453257X-RAY DIFFRACTION100
1.2561-1.2790.11361720.09113271X-RAY DIFFRACTION99
1.279-1.30360.10231710.08833256X-RAY DIFFRACTION100
1.3036-1.33020.10591730.08693285X-RAY DIFFRACTION100
1.3302-1.35910.11321720.09183265X-RAY DIFFRACTION100
1.3591-1.39070.11781740.09133300X-RAY DIFFRACTION100
1.3907-1.42550.12031710.09213261X-RAY DIFFRACTION99
1.4255-1.4640.11711730.09373279X-RAY DIFFRACTION99
1.464-1.50710.1111710.09233258X-RAY DIFFRACTION99
1.5071-1.55570.10981720.09193256X-RAY DIFFRACTION99
1.5557-1.61130.1141700.09643238X-RAY DIFFRACTION98
1.6113-1.67580.11541710.10223237X-RAY DIFFRACTION98
1.6758-1.75210.12481710.10663247X-RAY DIFFRACTION98
1.7521-1.84440.11841720.10943273X-RAY DIFFRACTION98
1.8444-1.95990.1221690.11423223X-RAY DIFFRACTION98
1.9599-2.11110.13261720.11863265X-RAY DIFFRACTION98
2.1111-2.32340.14321710.12273239X-RAY DIFFRACTION98
2.3234-2.65920.16461710.13493248X-RAY DIFFRACTION97
2.6592-3.34870.16051740.14543303X-RAY DIFFRACTION98
3.3487-23.29390.13491790.13273409X-RAY DIFFRACTION99

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