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- PDB-3bmn: Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bmn | ||||||
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Title | Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor (Compound AX3) | ||||||
![]() | (Pteridine reductase) x 2 | ||||||
![]() | OXIDOREDUCTASE / pteridine reductase / ptr1 / trypanosoma brucei / short chain dehydrogenase / inhibitor | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Martini, V.P. / Iulek, J. / Tulloch, L.B. / Hunter, W.N. | ||||||
![]() | ![]() Title: Structure-based design of pteridine reductase inhibitors targeting african sleeping sickness and the leishmaniases. Authors: Tulloch, L.B. / Martini, V.P. / Iulek, J. / Huggan, J.K. / Lee, J.H. / Gibson, C.L. / Smith, T.K. / Suckling, C.J. / Hunter, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 216.1 KB | Display | ![]() |
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PDB format | ![]() | 180.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 49.4 KB | Display | |
Data in CIF | ![]() | 66.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bmcC ![]() 3bmoC ![]() 3bmqC ![]() 3jq6C ![]() 3jq7C ![]() 3jq8C ![]() 3jq9C ![]() 3jqaC ![]() 3jqbC ![]() 3jqcC ![]() 3jqdC ![]() 3jqeC ![]() 3jqfC ![]() 3jqgC ![]() 3bms ![]() 3bmt 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 3
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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 30685.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 30669.791 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 6 types, 558 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/AX3.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AX3.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-AX3 / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | ChemComp-ACT / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 2-3M sodium acetate, 10-100mM sodium citrate, pH 4.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.98→75.59 Å / Num. obs: 64386 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.881 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS All of the 17 related structures are expressed from the same DNA construct, which encodes CYS at positions 59 and 168. Crystals harvested ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS All of the 17 related structures are expressed from the same DNA construct, which encodes CYS at positions 59 and 168. Crystals harvested within a couple of days of formation contain CYS at positions 59 and 168. However these two residues appear quite reactive and over time become oxidised to CSX, as determined by the emergence in older crystals of electron density for the OD atom. Sometimes CYS168 reacts with DTT in the crystallisation buffer, covalently linking the two molecules by an S-S bond
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.048 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→75.59 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.98→2.031 Å / Total num. of bins used: 20
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