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- PDB-6sbl: Human Carbonic Anhydrase II in complex with 4-hexylbenzenesulfonamide -

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Basic information

Entry
Database: PDB / ID: 6sbl
TitleHuman Carbonic Anhydrase II in complex with 4-hexylbenzenesulfonamide
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 / 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 / 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 / CITRATE ANION / : / 4-hexylbenzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 Å
AuthorsGloeckner, S. / Ngo, K. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Human Carbonic Anhydrase II in complex with 4-hexylbenzenesulfonamide
Authors: Gloeckner, S. / Ngo, K. / Heine, A. / Klebe, G.
History
DepositionJul 21, 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)30,9849
Polymers29,8071
Non-polymers1,1788
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-40 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.339, 41.568, 72.026
Angle α, β, γ (deg.)90.000, 104.301, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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 , 8 types, 244 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2
#6: Chemical ChemComp-L4Q / 4-hexylbenzenesulfonamide


Mass: 241.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#8: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 40.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Sodium citrate 1.40 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: Jun 23, 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: 0.94→41.568 Å / Num. obs: 152258 / % possible obs: 96.5 % / Redundancy: 3.44 % / Biso Wilson estimate: 8.27 Å2 / CC1/2: 0.996 / Rsym value: 0.061 / Net I/σ(I): 10.39
Reflection shellResolution: 0.94→1 Å / Redundancy: 2.94 % / Mean I/σ(I) obs: 2.25 / Num. unique obs: 22843 / CC1/2: 0.871 / Rsym value: 0.301 / % possible all: 90.1

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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: 0.94→41.03 Å / SU ML: 0.0596 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 10.509
RfactorNum. reflection% reflectionSelection details
Rfree0.1365 7613 5 %Random selection of 5 %
Rwork0.1214 ---
obs0.1221 152252 96.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 12.33 Å2
Refinement stepCycle: LAST / Resolution: 0.94→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 47 236 2279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872604
X-RAY DIFFRACTIONf_angle_d1.15253595
X-RAY DIFFRACTIONf_chiral_restr0.0952367
X-RAY DIFFRACTIONf_plane_restr0.0082501
X-RAY DIFFRACTIONf_dihedral_angle_d12.8569969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.94-0.950.20642010.21113825X-RAY DIFFRACTION77.8
0.95-0.960.20452320.18694412X-RAY DIFFRACTION87.92
0.96-0.970.17962490.16624722X-RAY DIFFRACTION94.51
0.97-0.990.17642500.15134755X-RAY DIFFRACTION95.61
0.99-10.1622480.14474718X-RAY DIFFRACTION95.89
1-1.010.14972540.13524826X-RAY DIFFRACTION96.23
1.01-1.030.12482500.12424748X-RAY DIFFRACTION96.32
1.03-1.040.12422530.11954805X-RAY DIFFRACTION95.81
1.04-1.060.11732530.11054813X-RAY DIFFRACTION96.72
1.06-1.080.13082530.11014795X-RAY DIFFRACTION97.17
1.08-1.090.11982540.10274837X-RAY DIFFRACTION97.27
1.09-1.110.11552550.09954843X-RAY DIFFRACTION97.2
1.11-1.140.11992560.09254849X-RAY DIFFRACTION97.59
1.14-1.160.10062560.09114863X-RAY DIFFRACTION97.43
1.16-1.180.11482540.09614833X-RAY DIFFRACTION96.75
1.18-1.210.11492590.09514925X-RAY DIFFRACTION98.13
1.21-1.240.10512550.09844840X-RAY DIFFRACTION97.81
1.24-1.280.11312560.0994857X-RAY DIFFRACTION97.86
1.28-1.310.12382590.09684926X-RAY DIFFRACTION98.65
1.31-1.350.11342580.10414903X-RAY DIFFRACTION98.64
1.35-1.40.11592580.10274899X-RAY DIFFRACTION98.06
1.4-1.460.1152590.10594921X-RAY DIFFRACTION98.09
1.46-1.530.11312590.10274934X-RAY DIFFRACTION99.01
1.53-1.610.10972610.10284959X-RAY DIFFRACTION98.77
1.61-1.710.11642600.11144926X-RAY DIFFRACTION98.74
1.71-1.840.12422610.11634975X-RAY DIFFRACTION98.87
1.84-2.020.12852580.12044902X-RAY DIFFRACTION97.14
2.02-2.320.13562630.12214986X-RAY DIFFRACTION99.17
2.32-2.920.15612620.14084976X-RAY DIFFRACTION98.44
2.92-41.030.17212670.1465066X-RAY DIFFRACTION97.91

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