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- PDB-6bm7: Crystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bm7 | |||||||||
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Title | Crystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodimer in complex with pyrimidineamine inhibitor UTSAM568 | |||||||||
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![]() | LYASE/LYASE INHIBITOR / AdoMetDC / prozyme / decarboxylase / Trypanosoma / inhibitor / LYASE-LYASE INHIBITOR complex | |||||||||
Function / homology | ![]() trypanothione biosynthetic process / positive regulation of spermidine biosynthetic process / spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / positive regulation of catalytic activity / spermidine biosynthetic process / S-adenosylmethionine metabolic process / catalytic complex / enzyme activator activity ...trypanothione biosynthetic process / positive regulation of spermidine biosynthetic process / spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / positive regulation of catalytic activity / spermidine biosynthetic process / S-adenosylmethionine metabolic process / catalytic complex / enzyme activator activity / protein heterodimerization activity / enzyme binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Volkov, O.A. / Chen, Z. / Phillips, M.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Species-Selective Pyrimidineamine Inhibitors of Trypanosoma brucei S-Adenosylmethionine Decarboxylase. Authors: Volkov, O.A. / Brockway, A.J. / Wring, S.A. / Peel, M. / Chen, Z. / Phillips, M.A. / De Brabander, J.K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 593.3 KB | Display | ![]() |
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PDB format | ![]() | 395.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 45.3 KB | Display | |
Data in CIF | ![]() | 60.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tvmS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-S-adenosylmethionine decarboxylase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 9754.132 Da / Num. of mol.: 2 / Fragment: UNP residues 1-85 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 927/4 GUTat10.1 / Gene: Tb927.6.4410, Tb927.6.4460 / Plasmid: pETDuet-1 / Production host: ![]() ![]() References: UniProt: Q587A7, adenosylmethionine decarboxylase #2: Protein | Mass: 32041.992 Da / Num. of mol.: 2 / Fragment: UNP residues 87-370 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 927/4 GUTat10.1 / Gene: Tb927.6.4410, Tb927.6.4460 / Plasmid: pETDuet-1 / Production host: ![]() ![]() References: UniProt: Q587A7, adenosylmethionine decarboxylase |
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-Protein , 1 types, 2 molecules EF
#3: Protein | Mass: 36343.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 927/4 GUTat10.1 / Plasmid: pETDuet-1 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 16 molecules 










#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-PG4 / | #9: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.63 % / Description: plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1 uL 4 mg/mL protein in crystallization buffer (50 mM Bis-Tris propane, pH 7.2, 50 mM sodium chloride, 4 mM TCEP, 2 mM putrescine, 0.5 mM N4-(3,5-dibromophenyl)-6-methylpyrimidine-2,4- ...Details: 1 uL 4 mg/mL protein in crystallization buffer (50 mM Bis-Tris propane, pH 7.2, 50 mM sodium chloride, 4 mM TCEP, 2 mM putrescine, 0.5 mM N4-(3,5-dibromophenyl)-6-methylpyrimidine-2,4-diamine [UTSAM568], 1% DMSO) + 1 uL reservoir solution (17% PEG6000, 100 mM Bis-Tris propane, pH 7.0) + 0.5 uL unliganded protein microseeds obtained using Seed-Bead method in stabilization solution (100 mM Bis-Tris propane, pH 8.9, 50 mM HEPES, pH 7.2, 19% PEG6000, 50 mM sodium chloride, 4 mM TCEP, 2 mM putrescine) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91905 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→50 Å / Num. obs: 30294 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 49.2238648407 Å2 / Rpim(I) all: 0.074 / Rrim(I) all: 0.194 / Net I/σ(I): 10 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.87 / Num. unique obs: 1466 / CC1/2: 0.712 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5TVM Resolution: 2.98→48.2623233532 Å / SU ML: 0.341675147008 / Cross valid method: FREE R-VALUE / σ(F): 1.33789805147 / Phase error: 26.3118648791
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.4151476361 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.98→48.2623233532 Å
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Refine LS restraints |
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LS refinement shell |
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