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- PDB-5u0d: Identification of a New Zinc Binding Chemotype by Fragment Screening -

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Basic information

Entry
Database: PDB / ID: 5u0d
TitleIdentification of a New Zinc Binding Chemotype by Fragment Screening
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Fragment screening / carbonic anhydrase
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 / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 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-7R7 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsPeat, T.S. / Poulsen, S.A. / Ren, B. / Dolezal, O. / Woods, L.A. / Mujumdar, P. / Chrysanthopoulos, P.K.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Identification of a New Zinc Binding Chemotype by Fragment Screening.
Authors: Chrysanthopoulos, P.K. / Mujumdar, P. / Woods, L.A. / Dolezal, O. / Ren, B. / Peat, T.S. / Poulsen, S.A.
History
DepositionNov 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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)29,7004
Polymers29,2891
Non-polymers4113
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.567, 41.341, 72.094
Angle α, β, γ (deg.)90.00, 104.47, 90.00
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 (E. coli) / 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-7R7 / (5R)-5-(2,4-dimethoxyphenyl)-2-sulfanylidene-1,3-oxazolidin-4-one


Mass: 253.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO4S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3; concentrated CA II at ~10 mg mL-1 was set up with seeding; dry compound was added to crystals ...Details: the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3; concentrated CA II at ~10 mg mL-1 was set up with seeding; dry compound was added to crystals several days before harvesting and data collection

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.59→41.3 Å / Num. obs: 32975 / % possible obs: 99.6 % / Redundancy: 7.2 % / CC1/2: 0.999 / Net I/σ(I): 21.6
Reflection shellResolution: 1.59→1.61 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.5 / CC1/2: 0.86 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4cq0

4cq0


Resolution: 1.59→41.3 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.852 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.071 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15449 1719 5.2 %RANDOM
Rwork0.11848 ---
obs0.12045 31243 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.669 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0.01 Å2
2---0.04 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.59→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 24 250 2333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192317
X-RAY DIFFRACTIONr_bond_other_d0.0020.022162
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9563164
X-RAY DIFFRACTIONr_angle_other_deg0.91735030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4175294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91724.86107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98115396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.204158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212710
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02540
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3961.2861122
X-RAY DIFFRACTIONr_mcbond_other1.361.2841121
X-RAY DIFFRACTIONr_mcangle_it1.7291.9391431
X-RAY DIFFRACTIONr_mcangle_other1.7471.941432
X-RAY DIFFRACTIONr_scbond_it2.1071.5691195
X-RAY DIFFRACTIONr_scbond_other2.1071.571195
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4572.2281733
X-RAY DIFFRACTIONr_long_range_B_refined2.81116.1632627
X-RAY DIFFRACTIONr_long_range_B_other2.8116.1682628
X-RAY DIFFRACTIONr_rigid_bond_restr1.81634479
X-RAY DIFFRACTIONr_sphericity_free20.7465146
X-RAY DIFFRACTIONr_sphericity_bonded7.29254504
LS refinement shellResolution: 1.588→1.629 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 106 -
Rwork0.169 2219 -
obs--95.6 %

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