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- PDB-6sdl: Human Carbonic Anhydrase II in complex with (R)-N-(3-(1H-indol-1-... -

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Basic information

Entry
Database: PDB / ID: 6sdl
TitleHuman Carbonic Anhydrase II in complex with (R)-N-(3-(1H-indol-1-yl)-2-methylpropyl)-4-sulfamoylbenzamide
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 / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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-SBR / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsGloeckner, S. / Gerber, H.D. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Human Carbonic Anhydrase II in complex with (R)-N-(3-(1H-indol-1-yl)-2-methylpropyl)-4-sulfamoylbenzamide
Authors: Gloeckner, S. / Gerber, H.D. / Heine, A. / Klebe, G.
History
DepositionJul 28, 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)30,9027
Polymers29,8071
Non-polymers1,0966
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-77 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.323, 41.696, 72.103
Angle α, β, γ (deg.)90.000, 104.321, 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, 219 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#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-SBR / (R)-N-(3-INDOL-1-YL-2-METHYL-PROPYL)-4-SULFAMOYL-BENZAMIDE


Mass: 371.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O3S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
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: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: May 17, 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: 1.08→41.696 Å / Num. obs: 101798 / % possible obs: 97.3 % / Redundancy: 3.71 % / Biso Wilson estimate: 9.86 Å2 / CC1/2: 0.994 / Rsym value: 0.089 / Net I/σ(I): 7.34
Reflection shellResolution: 1.08→1.15 Å / Mean I/σ(I) obs: 1.96 / Num. unique obs: 15740 / CC1/2: 0.815 / Rsym value: 0.45

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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: 1.08→39.94 Å / SU ML: 0.0851 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.3318
RfactorNum. reflection% reflectionSelection details
Rfree0.154 5089 5 %Random selection of 5 %
Rwork0.1363 ---
obs0.1372 101793 97.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.07 Å2
Refinement stepCycle: LAST / Resolution: 1.08→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 39 213 2248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062443
X-RAY DIFFRACTIONf_angle_d0.93863364
X-RAY DIFFRACTIONf_chiral_restr0.0808344
X-RAY DIFFRACTIONf_plane_restr0.0063469
X-RAY DIFFRACTIONf_dihedral_angle_d12.434898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.090.2171530.20952921X-RAY DIFFRACTION88.49
1.09-1.10.1991600.183041X-RAY DIFFRACTION93.11
1.1-1.120.18081650.183129X-RAY DIFFRACTION94.36
1.12-1.130.17611640.19543118X-RAY DIFFRACTION95.8
1.13-1.150.16041700.14883230X-RAY DIFFRACTION96.81
1.15-1.160.17281700.1483222X-RAY DIFFRACTION97.64
1.16-1.180.17231690.15363211X-RAY DIFFRACTION97.89
1.18-1.20.17091690.14043217X-RAY DIFFRACTION97.61
1.2-1.220.17231690.1453203X-RAY DIFFRACTION97.48
1.22-1.240.19361690.17353212X-RAY DIFFRACTION96.9
1.24-1.260.1781650.15523138X-RAY DIFFRACTION95.99
1.26-1.280.20191710.17383251X-RAY DIFFRACTION98
1.28-1.30.18341700.15563234X-RAY DIFFRACTION98.5
1.3-1.330.15521710.12853250X-RAY DIFFRACTION98.56
1.33-1.360.14011720.11863258X-RAY DIFFRACTION98.37
1.36-1.390.15591710.12513260X-RAY DIFFRACTION98.45
1.39-1.430.1411700.1123232X-RAY DIFFRACTION98.61
1.43-1.470.13711740.1153303X-RAY DIFFRACTION98.83
1.47-1.510.14261720.11673265X-RAY DIFFRACTION99.08
1.51-1.560.14431710.12033255X-RAY DIFFRACTION98.76
1.56-1.610.12831710.10263240X-RAY DIFFRACTION97.88
1.61-1.680.1411670.10743169X-RAY DIFFRACTION95.56
1.68-1.750.13721720.11043281X-RAY DIFFRACTION99.14
1.75-1.850.12991750.11883311X-RAY DIFFRACTION99.23
1.85-1.960.14021700.13143231X-RAY DIFFRACTION97.87
1.96-2.110.13031730.12653289X-RAY DIFFRACTION98.55
2.11-2.330.15771730.13583281X-RAY DIFFRACTION98.26
2.33-2.660.1621730.13943288X-RAY DIFFRACTION98.49
2.66-3.350.17071700.14873235X-RAY DIFFRACTION96.3
3.35-39.940.14721800.143429X-RAY DIFFRACTION99.39

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