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- PDB-6rit: Human Carbonic Anhydrase II in complex with 2-Fluorobenzenesulfonamide -

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Basic information

Entry
Database: PDB / ID: 6rit
TitleHuman Carbonic Anhydrase II in complex with 2-Fluorobenzenesulfonamide
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-CARBOXYPHENYL)(CHLORO)MERCURY / beta-D-glucopyranose / 2-fluorobenzenesulfonamide / alpha-D-glucopyranose / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.007 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: Biomolecules / Year: 2020
Title: The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II.
Authors: Glockner, S. / Ngo, K. / Wagner, B. / Heine, A. / Klebe, G.
History
DepositionApr 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Jan 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)31,3219
Polymers29,8071
Non-polymers1,5148
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-23 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.474, 41.639, 72.527
Angle α, β, γ (deg.)90.00, 104.43, 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 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

#2: 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, 231 molecules

#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2 / Comment: protease inhibitor*YM
#6: Chemical ChemComp-FBV / 2-fluorobenzenesulfonamide


Mass: 175.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6FNO2S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulfate 2.7 M, TRIS 0.1 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: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2018 / Details: Sagitally bended Si(111) crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.007→41.639 Å / Num. obs: 126668 / % possible obs: 97.5 % / Redundancy: 3.61 % / Biso Wilson estimate: 6.5 Å2 / CC1/2: 0.999 / Rsym value: 0.0492 / Net I/σ(I): 4.9
Reflection shellResolution: 1.01→1.07 Å / Redundancy: 3.36 % / Num. unique obs: 19712 / CC1/2: 0.891 / Rsym value: 0.394 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.007→40.122 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 10.71
RfactorNum. reflection% reflectionSelection details
Rfree0.14 6334 5 %Random selection of 5 %
Rwork0.125 ---
obs0.1257 126658 97.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.007→40.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 70 226 2316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092755
X-RAY DIFFRACTIONf_angle_d1.0953802
X-RAY DIFFRACTIONf_dihedral_angle_d13.0921032
X-RAY DIFFRACTIONf_chiral_restr0.09390
X-RAY DIFFRACTIONf_plane_restr0.008526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0065-1.0180.6181780.59133386X-RAY DIFFRACTION83
1.018-1.030.40362100.42173973X-RAY DIFFRACTION97
1.03-1.04250.34942090.34613977X-RAY DIFFRACTION97
1.0425-1.05570.30412080.28353946X-RAY DIFFRACTION97
1.0557-1.06960.19662110.19714016X-RAY DIFFRACTION98
1.0696-1.08430.17382110.14944003X-RAY DIFFRACTION98
1.0843-1.09980.12232110.11074019X-RAY DIFFRACTION98
1.0998-1.11620.10912120.09984011X-RAY DIFFRACTION98
1.1162-1.13360.12692090.09343976X-RAY DIFFRACTION98
1.1336-1.15220.11912120.09614027X-RAY DIFFRACTION98
1.1522-1.17210.12692100.10393999X-RAY DIFFRACTION98
1.1721-1.19340.12662090.10473966X-RAY DIFFRACTION97
1.1934-1.21630.14252140.11024073X-RAY DIFFRACTION99
1.2163-1.24120.12792130.10824051X-RAY DIFFRACTION98
1.2412-1.26820.13022120.10664018X-RAY DIFFRACTION98
1.2682-1.29770.1162140.094063X-RAY DIFFRACTION98
1.2977-1.33010.09432110.08634017X-RAY DIFFRACTION98
1.3301-1.36610.11632120.09324016X-RAY DIFFRACTION98
1.3661-1.40630.11712110.09244026X-RAY DIFFRACTION98
1.4063-1.45170.11162120.09484022X-RAY DIFFRACTION97
1.4517-1.50360.10872130.09254034X-RAY DIFFRACTION99
1.5036-1.56380.11582150.09644093X-RAY DIFFRACTION99
1.5638-1.63490.11252130.10094056X-RAY DIFFRACTION98
1.6349-1.72110.12282130.10184044X-RAY DIFFRACTION98
1.7211-1.8290.12422140.10534060X-RAY DIFFRACTION98
1.829-1.97020.132110.11294007X-RAY DIFFRACTION97
1.9702-2.16840.1162150.11714098X-RAY DIFFRACTION99
2.1684-2.48220.1392180.1264129X-RAY DIFFRACTION99
2.4822-3.12710.16022140.14584075X-RAY DIFFRACTION98
3.1271-40.15340.15272190.14094143X-RAY DIFFRACTION97

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