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- PDB-6sg6: Human Carbonic Anhydrase II in complex with furan-containing benz... -

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Basic information

Entry
Database: PDB / ID: 6sg6
TitleHuman Carbonic Anhydrase II in complex with 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 / Chem-LC8 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Human Carbonic Anhydrase II in complex with 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)30,6286
Polymers29,8071
Non-polymers8215
Water4,071226
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-7 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.336, 41.664, 72.230
Angle α, β, γ (deg.)90.000, 104.419, 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 , 6 types, 231 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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 / Comment: protease inhibitor*YM
#5: Chemical ChemComp-LC8 / 4-(furan-2-ylmethylamino)-3-nitro-benzenesulfonamide


Mass: 297.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11N3O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: 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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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: 2.14 Å3/Da / Density % sol: 42.45 %
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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2018
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: 0.98→41.664 Å / Num. obs: 136715 / % possible obs: 97.7 % / Redundancy: 3.57 % / Biso Wilson estimate: 9.27 Å2 / CC1/2: 0.997 / Rsym value: 0.057 / Net I/σ(I): 10.85
Reflection shellResolution: 0.98→1.04 Å / Mean I/σ(I) obs: 2.35 / Num. unique obs: 21571 / CC1/2: 0.853 / Rsym value: 0.363

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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: 0.98→39.98 Å / SU ML: 0.0718 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 10.7019
RfactorNum. reflection% reflectionSelection details
Rfree0.1354 6835 5 %Random selection of 5 %
Rwork0.1219 ---
obs0.1226 136703 97.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.4 Å2
Refinement stepCycle: LAST / Resolution: 0.98→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 36 226 2263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642493
X-RAY DIFFRACTIONf_angle_d0.96113436
X-RAY DIFFRACTIONf_chiral_restr0.0819355
X-RAY DIFFRACTIONf_plane_restr0.0074481
X-RAY DIFFRACTIONf_dihedral_angle_d14.9255917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-0.990.20912170.20724130X-RAY DIFFRACTION92.98
0.99-10.20882220.20084216X-RAY DIFFRACTION95.73
1-1.010.22512240.18554251X-RAY DIFFRACTION96.13
1.01-1.030.18092210.18024211X-RAY DIFFRACTION96.43
1.03-1.040.18532260.16094293X-RAY DIFFRACTION96.97
1.04-1.060.16052240.14134238X-RAY DIFFRACTION96.71
1.06-1.070.13382220.12594221X-RAY DIFFRACTION95.59
1.07-1.090.13632270.11414311X-RAY DIFFRACTION97.55
1.09-1.10.13182250.11324283X-RAY DIFFRACTION97.55
1.1-1.120.1142270.10554310X-RAY DIFFRACTION97.51
1.12-1.140.11512270.09474326X-RAY DIFFRACTION97.68
1.14-1.160.10842280.09424325X-RAY DIFFRACTION97.96
1.16-1.180.10392260.09394298X-RAY DIFFRACTION97.44
1.18-1.210.1212250.09474283X-RAY DIFFRACTION97.28
1.21-1.230.10852260.09524299X-RAY DIFFRACTION97.54
1.23-1.260.11542320.09474399X-RAY DIFFRACTION98.7
1.26-1.290.11392270.09474323X-RAY DIFFRACTION98.48
1.29-1.330.10972290.09384338X-RAY DIFFRACTION98.75
1.33-1.370.11222310.09834398X-RAY DIFFRACTION98.95
1.37-1.410.11892320.09654404X-RAY DIFFRACTION99.06
1.41-1.460.1052280.09934323X-RAY DIFFRACTION98.29
1.46-1.520.11532310.09854390X-RAY DIFFRACTION98.95
1.52-1.590.12432300.09914380X-RAY DIFFRACTION99.16
1.59-1.680.11712330.1034416X-RAY DIFFRACTION99.36
1.68-1.780.13292320.11044409X-RAY DIFFRACTION99.25
1.78-1.920.12772320.11864406X-RAY DIFFRACTION98.72
1.92-2.110.13332280.12334347X-RAY DIFFRACTION97.8
2.11-2.420.12222330.12744410X-RAY DIFFRACTION98.89
2.42-3.040.18012330.1484435X-RAY DIFFRACTION98.65
3.04-39.980.14672370.13964495X-RAY DIFFRACTION97.87

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