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- PDB-5g5v: Crystal structure of T. brucei PDE-B1 catalytic domain with inhib... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5g5v | ||||||
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Title | Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-038 | ||||||
![]() | PHOSPHODIESTERASE B1 | ||||||
![]() | HYDROLASE / PARASITIC PDE / AFRICAN TRYPANOSOMIASIS / SLEEPING SICKNESS | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / cGMP catabolic process / axoneme / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / cell morphogenesis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singh, A.K. / Brown, D.G. | ||||||
![]() | ![]() Title: Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity. Authors: Blaazer, A.R. / Singh, A.K. / de Heuvel, E. / Edink, E. / Orrling, K.M. / Veerman, J.J.N. / van den Bergh, T. / Jansen, C. / Balasubramaniam, E. / Mooij, W.J. / Custers, H. / Sijm, M. / ...Authors: Blaazer, A.R. / Singh, A.K. / de Heuvel, E. / Edink, E. / Orrling, K.M. / Veerman, J.J.N. / van den Bergh, T. / Jansen, C. / Balasubramaniam, E. / Mooij, W.J. / Custers, H. / Sijm, M. / Tagoe, D.N.A. / Kalejaiye, T.D. / Munday, J.C. / Tenor, H. / Matheeussen, A. / Wijtmans, M. / Siderius, M. / de Graaf, C. / Maes, L. / de Koning, H.P. / Bailey, D.S. / Sterk, G.J. / de Esch, I.J.P. / Brown, D.G. / Leurs, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.4 KB | Display | ![]() |
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PDB format | ![]() | 123.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 858.6 KB | Display | ![]() |
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Full document | ![]() | 860.2 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 43.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g2bC ![]() 5g57C ![]() 5l8cC ![]() 5l8yC ![]() 5l9hC ![]() 5laqC ![]() 5lboC ![]() 4i15S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40623.340 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 565-918 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8WQX9, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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-Non-polymers , 7 types, 475 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GAI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/8Z4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GAI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/8Z4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GAI / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | ChemComp-8Z4 / ( | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.5 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, 0.4 M SODIUM FORMATE, 0.3 M GUANIDINE, 0.1 M MES PH 6.5; VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 4 DEGREES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: Aug 3, 2015 / Details: CRL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→88.58 Å / Num. obs: 90889 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4I15 Resolution: 1.8→88.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.348 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→88.58 Å
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Refine LS restraints |
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