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- PDB-6s9g: Human Carbonic Anhydrase II in complex with fluorinated benzenesu... -

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Basic information

Entry
Database: PDB / ID: 6s9g
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 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, 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 / : / Chem-L1Q / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsGloeckner, S. / Ngo, K. / 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
DepositionJul 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_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
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)31,1527
Polymers29,8071
Non-polymers1,3466
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-28 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.337, 41.456, 72.129
Angle α, β, γ (deg.)90.000, 104.455, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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
#3: 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, 270 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2
#5: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#6: Chemical ChemComp-L1Q / 2,3,5,6-tetrakis(fluoranyl)-4-propyl-benzenesulfonamide


Mass: 271.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9F4NO2S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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, hanging drop
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: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: May 3, 2017
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: 1.14→41.46 Å / Num. obs: 87774 / % possible obs: 98.9 % / Redundancy: 3.63 % / Biso Wilson estimate: 11.24 Å2 / CC1/2: 0.999 / Rsym value: 0.053 / Net I/σ(I): 11.19
Reflection shellResolution: 1.14→1.21 Å / Redundancy: 3.56 % / Mean I/σ(I) obs: 2.09 / Num. unique obs: 13942 / CC1/2: 0.802 / Rsym value: 0.471 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.14→23.81 Å / SU ML: 0.081 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.7411
RfactorNum. reflection% reflectionSelection details
Rfree0.1471 4388 5 %Random selection of 5 %
Rwork0.1229 ---
obs0.1241 87761 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.82 Å2
Refinement stepCycle: LAST / Resolution: 1.14→23.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 56 265 2326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632348
X-RAY DIFFRACTIONf_angle_d0.9843230
X-RAY DIFFRACTIONf_chiral_restr0.08336
X-RAY DIFFRACTIONf_plane_restr0.0069451
X-RAY DIFFRACTIONf_dihedral_angle_d14.2941863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.20271300.19912482X-RAY DIFFRACTION89.36
1.15-1.170.22371470.1892779X-RAY DIFFRACTION99.59
1.17-1.180.21781470.1822795X-RAY DIFFRACTION99.46
1.18-1.190.19381470.18162786X-RAY DIFFRACTION99.63
1.19-1.210.1941470.1782797X-RAY DIFFRACTION99.8
1.21-1.230.20311440.16932746X-RAY DIFFRACTION99.76
1.23-1.240.20021480.15972801X-RAY DIFFRACTION99.8
1.24-1.260.17391470.15532788X-RAY DIFFRACTION99.63
1.26-1.280.15211460.15282790X-RAY DIFFRACTION99.19
1.28-1.30.1581440.1352734X-RAY DIFFRACTION99.69
1.3-1.330.16221480.1282808X-RAY DIFFRACTION99.73
1.33-1.350.14181470.12492786X-RAY DIFFRACTION99.69
1.35-1.380.14881460.11842782X-RAY DIFFRACTION99.49
1.38-1.40.1491470.11612794X-RAY DIFFRACTION99.53
1.4-1.430.14391470.1132780X-RAY DIFFRACTION99.66
1.43-1.470.13651460.10822777X-RAY DIFFRACTION99.22
1.47-1.50.12821470.09942794X-RAY DIFFRACTION99.43
1.5-1.550.13021460.09722785X-RAY DIFFRACTION99.09
1.55-1.590.1141460.09992769X-RAY DIFFRACTION98.85
1.59-1.640.11721470.09772796X-RAY DIFFRACTION99.39
1.64-1.70.13591470.10072782X-RAY DIFFRACTION99.39
1.7-1.770.13421470.09942795X-RAY DIFFRACTION99.06
1.77-1.850.13021480.10282812X-RAY DIFFRACTION99.26
1.85-1.950.11641450.10322751X-RAY DIFFRACTION98.97
1.95-2.070.13371460.11312789X-RAY DIFFRACTION98.59
2.07-2.230.11731470.11232783X-RAY DIFFRACTION98.49
2.23-2.450.13321460.11442782X-RAY DIFFRACTION98.52
2.45-2.810.17691470.12782780X-RAY DIFFRACTION98.09
2.81-3.530.15171490.13252845X-RAY DIFFRACTION99.44
3.53-23.810.15521520.12872885X-RAY DIFFRACTION98.7

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