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- PDB-6roe: Human Carbonic Anhydrase II in complex with fluorinated benzenesu... -

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Basic information

Entry
Database: PDB / ID: 6roe
TitleHuman Carbonic Anhydrase II in complex with fluorinated 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 / 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 / 2,6-DIFLUOROBENZENESULFONAMIDE / alpha-D-glucopyranose / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.939 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
DepositionMay 12, 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)31,3579
Polymers29,8071
Non-polymers1,5508
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-61 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.364, 41.401, 72.278
Angle α, β, γ (deg.)90.00, 104.53, 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
#3: 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, 210 molecules

#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#6: 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
#7: Chemical ChemComp-FBT / 2,6-DIFLUOROBENZENESULFONAMIDE


Mass: 193.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5F2NO2S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 40.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulfate 2.7 M, TRIS 0.1 M, 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: Sep 28, 2017 / 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: 0.939→41.401 Å / Num. obs: 152196 / % possible obs: 96.5 % / Redundancy: 3.49 % / Biso Wilson estimate: 7.3 Å2 / CC1/2: 0.999 / Rsym value: 0.043 / Net I/σ(I): 14.83
Reflection shellResolution: 0.94→1 Å / Redundancy: 3.03 % / Mean I/σ(I) obs: 3.62 / Num. unique obs: 23134 / CC1/2: 0.954 / Rsym value: 0.187 / % possible all: 91.5

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Processing

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

3ks3


Resolution: 0.939→35.631 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 8.32
RfactorNum. reflection% reflectionSelection details
Rfree0.1185 7610 5 %Random selection of 5 %
Rwork0.1096 ---
obs0.1101 152179 96.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.939→35.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 72 205 2284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062739
X-RAY DIFFRACTIONf_angle_d0.9693796
X-RAY DIFFRACTIONf_dihedral_angle_d14.7141030
X-RAY DIFFRACTIONf_chiral_restr0.081389
X-RAY DIFFRACTIONf_plane_restr0.007540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9393-0.950.17471880.15283573X-RAY DIFFRACTION73
0.95-0.96120.1542320.14074405X-RAY DIFFRACTION89
0.9612-0.97290.14862610.13494962X-RAY DIFFRACTION99
0.9729-0.98520.1382600.12784940X-RAY DIFFRACTION99
0.9852-0.99820.12922550.11864830X-RAY DIFFRACTION98
0.9982-1.01190.13192550.11334861X-RAY DIFFRACTION98
1.0119-1.02630.11512540.10154812X-RAY DIFFRACTION97
1.0263-1.04160.10762410.09384587X-RAY DIFFRACTION92
1.0416-1.05790.12630.08415000X-RAY DIFFRACTION100
1.0579-1.07530.09392590.08364915X-RAY DIFFRACTION99
1.0753-1.09380.09682600.0854941X-RAY DIFFRACTION99
1.0938-1.11370.10112600.08444935X-RAY DIFFRACTION99
1.1137-1.13510.09252550.07584854X-RAY DIFFRACTION98
1.1351-1.15830.08392540.07874826X-RAY DIFFRACTION97
1.1583-1.18350.09772510.07954754X-RAY DIFFRACTION95
1.1835-1.2110.09282610.07994968X-RAY DIFFRACTION99
1.211-1.24130.0952580.08154899X-RAY DIFFRACTION99
1.2413-1.27490.09622590.08674928X-RAY DIFFRACTION99
1.2749-1.31240.09172600.08454933X-RAY DIFFRACTION99
1.3124-1.35470.10812540.08744835X-RAY DIFFRACTION97
1.3547-1.40310.10272480.09264701X-RAY DIFFRACTION94
1.4031-1.45930.10282540.09614839X-RAY DIFFRACTION96
1.4593-1.52570.10042580.09264892X-RAY DIFFRACTION98
1.5257-1.60620.09932570.09734889X-RAY DIFFRACTION98
1.6062-1.70680.10052560.10154859X-RAY DIFFRACTION97
1.7068-1.83860.12482540.10714830X-RAY DIFFRACTION97
1.8386-2.02360.12742540.1124819X-RAY DIFFRACTION95
2.0236-2.31640.12552620.12014975X-RAY DIFFRACTION99
2.3164-2.91820.14742610.1364969X-RAY DIFFRACTION98
2.9182-35.65620.13962660.13945038X-RAY DIFFRACTION97

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