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- PDB-6sfu: Human Carbonic Anhydrase II in complex with a furan-containing be... -

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Basic information

Entry
Database: PDB / ID: 6sfu
TitleHuman Carbonic Anhydrase II in complex with a furan-containing 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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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 / : / 4-(furan-2-ylmethylamino)benzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Human Carbonic Anhydrase II in complex with a furan-containing benzenesulfonamide
Authors: Gloeckner, S. / Heine, A. / Klebe, G.
History
DepositionAug 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)31,0589
Polymers29,8071
Non-polymers1,2528
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-42 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.447, 41.620, 72.401
Angle α, β, γ (deg.)90.000, 104.564, 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 , 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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Non-polymers , 7 types, 239 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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-LBQ / 4-(furan-2-ylmethylamino)benzenesulfonamide


Mass: 252.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O3S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Sodium citrate 1.4 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: ELETTRA / Beamline: 11.2C / Wavelength: 0.885 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 1.039→41.62 Å / Num. obs: 117443 / % possible obs: 99.6 % / Redundancy: 7.02 % / Biso Wilson estimate: 7.6 Å2 / CC1/2: 0.999 / Rsym value: 0.073 / Net I/σ(I): 14.18
Reflection shellResolution: 1.04→1.1 Å / Mean I/σ(I) obs: 3.12 / Num. unique obs: 18662 / CC1/2: 0.902 / Rsym value: 0.463 / % possible all: 98.4

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Processing

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

3ks3


Resolution: 1.04→29.24 Å / SU ML: 0.0788 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.1431
RfactorNum. reflection% reflectionSelection details
Rfree0.1383 5872 5 %Random selection of 5 %
Rwork0.1255 ---
obs0.1261 117414 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.55 Å2
Refinement stepCycle: LAST / Resolution: 1.04→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 47 231 2288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062483
X-RAY DIFFRACTIONf_angle_d0.93193424
X-RAY DIFFRACTIONf_chiral_restr0.0817351
X-RAY DIFFRACTIONf_plane_restr0.0067487
X-RAY DIFFRACTIONf_dihedral_angle_d14.06925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.050.18141800.17753413X-RAY DIFFRACTION93.06
1.05-1.060.16831990.14973771X-RAY DIFFRACTION99.75
1.06-1.080.16521910.14163631X-RAY DIFFRACTION99.82
1.08-1.090.15781970.13633735X-RAY DIFFRACTION99.87
1.09-1.10.15361940.15373689X-RAY DIFFRACTION99.85
1.1-1.120.19351970.1443738X-RAY DIFFRACTION99.87
1.12-1.130.1361930.13273669X-RAY DIFFRACTION99.84
1.13-1.150.16381970.1253745X-RAY DIFFRACTION99.82
1.15-1.170.13631930.12333675X-RAY DIFFRACTION99.72
1.17-1.190.14391970.11583731X-RAY DIFFRACTION99.52
1.19-1.210.1281950.1123702X-RAY DIFFRACTION99.67
1.21-1.230.12071930.10773669X-RAY DIFFRACTION99.92
1.23-1.250.13171970.10763743X-RAY DIFFRACTION99.82
1.25-1.280.12231940.10673684X-RAY DIFFRACTION99.82
1.28-1.310.11821950.10273717X-RAY DIFFRACTION99.9
1.31-1.340.11761970.10783735X-RAY DIFFRACTION99.95
1.34-1.370.12881980.10953757X-RAY DIFFRACTION100
1.37-1.410.13861940.10523694X-RAY DIFFRACTION99.87
1.41-1.450.12371970.10543735X-RAY DIFFRACTION99.9
1.45-1.50.12021940.10393692X-RAY DIFFRACTION99.97
1.5-1.550.12521970.09893755X-RAY DIFFRACTION99.92
1.55-1.610.11621970.10253730X-RAY DIFFRACTION100
1.61-1.690.11671970.10723746X-RAY DIFFRACTION100
1.69-1.780.12951970.11423738X-RAY DIFFRACTION99.95
1.78-1.890.12361970.11493738X-RAY DIFFRACTION99.85
1.89-2.030.13271970.12513741X-RAY DIFFRACTION99.77
2.03-2.240.12261980.12663754X-RAY DIFFRACTION99.77
2.24-2.560.15281970.1343753X-RAY DIFFRACTION99.87
2.56-3.230.15151990.14953787X-RAY DIFFRACTION99.85
3.23-29.240.15512040.14533875X-RAY DIFFRACTION99.88

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