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- PDB-6b4d: Crystal structure of human carbonic anhydrase II in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6b4d
TitleCrystal structure of human carbonic anhydrase II in complex with a heteroaryl-pyrazole carboxylic acid derivative.
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic anhydrase / inhibitor / carboxylic acid
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 / arylesterase activity / regulation of chloride transport / 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 / arylesterase activity / regulation of chloride transport / 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 II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-53X / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.196 Å
AuthorsLomelino, C.L. / Mahon, B.P. / McKenna, R.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Exploring Heteroaryl-pyrazole Carboxylic Acids as Human Carbonic Anhydrase XII Inhibitors.
Authors: Cadoni, R. / Pala, N. / Lomelino, C. / Mahon, B.P. / McKenna, R. / Dallocchio, R. / Dessi, A. / Carcelli, M. / Rogolino, D. / Sanna, V. / Rassu, M. / Iaccarino, C. / Vullo, D. / Supuran, C.T. / Sechi, M.
History
DepositionSep 26, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 7, 2018ID: 5CJL
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 2023Group: 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

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5166
Polymers28,9331
Non-polymers5835
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-36 kcal/mol
Surface area11550 Å2
Unit cell
Length a, b, c (Å)42.359, 41.507, 72.333
Angle α, β, γ (deg.)90.000, 104.250, 90.000
Int Tables number4
Space group name H-MP1211

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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: 28932.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 339 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 / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-53X / 3-(1-ethyl-1H-indol-3-yl)-1-methyl-1H-pyrazole-5-carboxylic acid


Mass: 269.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15N3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50mM Tris HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.196→19.9 Å / Num. obs: 67580 / % possible obs: 91.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 8.57 Å2 / Net I/σ(I): 29.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10pre_2097refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3
Resolution: 1.196→19.9 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.21
RfactorNum. reflection% reflection
Rfree0.156 1983 2.93 %
Rwork0.1389 --
obs0.1394 67580 87.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.23 Å2 / Biso mean: 16.0164 Å2 / Biso min: 4.78 Å2
Refinement stepCycle: final / Resolution: 1.196→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 73 341 2463
Biso mean--25.85 28.96 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072213
X-RAY DIFFRACTIONf_angle_d1.1413013
X-RAY DIFFRACTIONf_chiral_restr0.086317
X-RAY DIFFRACTIONf_plane_restr0.012387
X-RAY DIFFRACTIONf_dihedral_angle_d16.677817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1963-1.22620.21331270.18984186431379
1.2262-1.25930.18941530.17764825497891
1.2593-1.29640.19491360.17364871500791
1.2964-1.33820.19531500.16324840499092
1.3382-1.3860.16761530.15294864501792
1.386-1.44150.15991450.15024867501291
1.4415-1.50710.14251530.14164825497891
1.5071-1.58650.14621390.13534810494990
1.5865-1.68590.15151450.13324830497590
1.6859-1.81590.13421530.13014771492489
1.8159-1.99850.14111430.12534714485789
1.9985-2.28740.13181400.11944691483187
2.2874-2.88050.12781360.13084560469685
2.8805-19.90260.1981100.14123943405372
Refinement TLS params.Method: refined / Origin x: -9.3657 Å / Origin y: -1.9615 Å / Origin z: 16.1139 Å
111213212223313233
T0.0529 Å2-0.0021 Å20.0003 Å2-0.0504 Å20.0023 Å2--0.0536 Å2
L0.5129 °2-0.0846 °2-0.0061 °2-0.4094 °20.0195 °2--0.3986 °2
S-0.0045 Å °-0.02 Å °0.0155 Å °-0.0218 Å °0.0012 Å °0.0027 Å °0.0159 Å °0.0102 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD2 - 347
4X-RAY DIFFRACTION1allD347
5X-RAY DIFFRACTION1allC1 - 2
6X-RAY DIFFRACTION1allE400
7X-RAY DIFFRACTION1allF1

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