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- PDB-6sey: Human Carbonic Anhydrase II in complex with aliphatically substit... -

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Basic information

Entry
Database: PDB / ID: 6sey
TitleHuman Carbonic Anhydrase II in complex with aliphatically substituted 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 / beta-D-glucopyranose / alpha-D-glucopyranose / : / 4-(4-oxidanylbutyl)benzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsGloeckner, S. / Ngo, K. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Human Carbonic Anhydrase II in complex with aliphatically substituted benzenesulfonamide
Authors: Gloeckner, S. / Ngo, K. / Heine, A. / Klebe, G.
History
DepositionJul 30, 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)31,4299
Polymers29,8071
Non-polymers1,6228
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-24 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.671, 41.842, 72.836
Angle α, β, γ (deg.)90.000, 104.681, 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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Sugars , 2 types, 3 molecules

#5: 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
#6: 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, 206 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-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-L9B / 4-(4-oxidanylbutyl)benzenesulfonamide


Mass: 229.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15NO3S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulfate 2.7 M, TRIS 0.1 M, saturated 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 PILATUS3 S 2M / Detector: PIXEL / Date: Jan 18, 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: 1.23→41.842 Å / Num. obs: 69652 / % possible obs: 97.2 % / Redundancy: 3.72 % / Biso Wilson estimate: 8.27 Å2 / CC1/2: 0.998 / Rsym value: 0.046 / Net I/σ(I): 17.66
Reflection shellResolution: 1.23→1.31 Å / Redundancy: 3.75 % / Mean I/σ(I) obs: 8.2 / Num. unique obs: 10672 / CC1/2: 0.984 / Rsym value: 0.135 / % possible all: 92.7

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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: 1.23→41.28 Å / SU ML: 0.0577 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 9.3564
RfactorNum. reflection% reflection
Rfree0.1249 3483 5 %
Rwork0.1099 --
obs0.1107 69646 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.92 Å2
Refinement stepCycle: LAST / Resolution: 1.23→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 75 201 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672314
X-RAY DIFFRACTIONf_angle_d0.96563178
X-RAY DIFFRACTIONf_chiral_restr0.0804339
X-RAY DIFFRACTIONf_plane_restr0.0067431
X-RAY DIFFRACTIONf_dihedral_angle_d12.1762857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.250.14741090.11022079X-RAY DIFFRACTION77.48
1.25-1.270.13141410.09332669X-RAY DIFFRACTION97.54
1.27-1.290.111360.08932585X-RAY DIFFRACTION97.49
1.29-1.310.10631410.0832677X-RAY DIFFRACTION98.19
1.31-1.330.12871390.08162637X-RAY DIFFRACTION97.34
1.33-1.350.11251400.0832656X-RAY DIFFRACTION98.07
1.35-1.380.11421390.08362654X-RAY DIFFRACTION97.25
1.38-1.40.10851380.08422619X-RAY DIFFRACTION98.01
1.4-1.430.11741360.08612583X-RAY DIFFRACTION95.4
1.43-1.460.11991410.08312673X-RAY DIFFRACTION98.39
1.46-1.50.10341400.07982670X-RAY DIFFRACTION98.49
1.5-1.530.10511410.08022676X-RAY DIFFRACTION98.88
1.53-1.580.11231410.08122687X-RAY DIFFRACTION99.09
1.58-1.620.11291410.08282680X-RAY DIFFRACTION98.84
1.62-1.680.11731420.08682696X-RAY DIFFRACTION98.78
1.68-1.740.11841400.08932650X-RAY DIFFRACTION98.31
1.74-1.80.10281410.0912681X-RAY DIFFRACTION98.77
1.8-1.890.10121420.09942697X-RAY DIFFRACTION98.82
1.89-1.990.11131370.10242607X-RAY DIFFRACTION95.28
1.99-2.110.12881410.1072684X-RAY DIFFRACTION99.12
2.11-2.270.12311440.11292720X-RAY DIFFRACTION99
2.27-2.50.12421430.12112729X-RAY DIFFRACTION99.31
2.5-2.860.14211420.13322702X-RAY DIFFRACTION98.65
2.86-3.610.15241410.14212666X-RAY DIFFRACTION96.79
3.61-41.280.13611470.13882786X-RAY DIFFRACTION98.23

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