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- PDB-6ypw: Crystal structure for the complex of human carbonic anhydrase II ... -

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Basic information

Entry
Database: PDB / ID: 6ypw
TitleCrystal structure for the complex of human carbonic anhydrase II and 4-((1-(2-(hydroxymethyl)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-3-yl)-1H-1,2,3-triazol-4-yl)methoxy)benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic Anhydrase Inhibitors / AZT / Telomerase Inhibitors / Cancer / Molecular hybrids / Click Chemistry / Triazole.
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 / zinc ion binding / extracellular exosome / 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
Chem-P75 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsAngeli, A. / Ferraroni, M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Mechanisms of the Antiproliferative and Antitumor Activity of Novel Telomerase-Carbonic Anhydrase Dual-Hybrid Inhibitors.
Authors: Plyasova, A.A. / Berrino, E. / Khan, I.I. / Veselovsky, A.V. / Pokrovsky, V.S. / Angeli, A. / Ferraroni, M. / Supuran, C.T. / Pokrovskaya, M.V. / Alexandrova, S.S. / Gladilina, Y.A. / ...Authors: Plyasova, A.A. / Berrino, E. / Khan, I.I. / Veselovsky, A.V. / Pokrovsky, V.S. / Angeli, A. / Ferraroni, M. / Supuran, C.T. / Pokrovskaya, M.V. / Alexandrova, S.S. / Gladilina, Y.A. / Sokolov, N.N. / Hilal, A. / Carta, F. / Zhdanov, D.D.
History
DepositionApr 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,8333
Polymers29,2891
Non-polymers5442
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.387, 41.358, 72.075
Angle α, β, γ (deg.)90.000, 104.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-P75 / 4-[[1-[(2~{S},3~{S},5~{R})-2-(hydroxymethyl)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]oxolan-3-yl]-1,2,3-triazol-4-yl]methoxy]benzenesulfonamide


Mass: 478.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N6O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.2 M sodium citrate, 50 mM Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→41.36 Å / Num. obs: 88794 / % possible obs: 90.7 % / Redundancy: 6.3 % / CC1/2: 0.999 / Net I/σ(I): 19.5
Reflection shellResolution: 1.1→1.11 Å / Num. unique obs: 2400 / CC1/2: 0.831 / % possible all: 49.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P58

3p58


Resolution: 1.1→41.09 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.661 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.132 4443 5 %RANDOM
Rwork0.1143 ---
obs0.1152 84333 90.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.11 Å2 / Biso mean: 12.45 Å2 / Biso min: 5.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.02 Å2
2--0.07 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.1→41.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 34 306 2398
Biso mean--15.55 25.1 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132203
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171981
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.6643004
X-RAY DIFFRACTIONr_angle_other_deg1.511.64638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0855270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21423.818110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.515364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.321157
X-RAY DIFFRACTIONr_chiral_restr0.1010.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
X-RAY DIFFRACTIONr_rigid_bond_restr2.32434184
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 189 -
Rwork0.189 3580 -
all-3769 -
obs--52.11 %

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