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- PDB-1njs: human GAR Tfase in complex with hydrolyzed form of 10-trifluoroac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1njs | ||||||
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Title | human GAR Tfase in complex with hydrolyzed form of 10-trifluoroacetyl-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid | ||||||
![]() | Phosphoribosylglycinamide formyltransferase | ||||||
![]() | TRANSFERASE / protein-cofactor analogue complex | ||||||
Function / homology | ![]() phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / adenine biosynthetic process / phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / phosphoribosylglycinamide formyltransferase 1 / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / 'de novo' XMP biosynthetic process / brainstem development ...phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / adenine biosynthetic process / phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / phosphoribosylglycinamide formyltransferase 1 / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / 'de novo' XMP biosynthetic process / brainstem development / Purine ribonucleoside monophosphate biosynthesis / glycine metabolic process / 'de novo' AMP biosynthetic process / GMP biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / : / tetrahydrofolate biosynthetic process / cerebellum development / : / cerebral cortex development / extracellular exosome / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / Desharnais, J. / Marsilje, T.H. / Li, C. / Hedrick, M.P. / Gooljarsingh, L.T. / Tavassoli, A. / Benkovic, S.J. / Olson, A.J. / Boger, D.L. / Wilson, I.A. | ||||||
![]() | ![]() Title: Rational Design, Synthesis, Evaluation, and Crystal Structure of a Potent Inhibitor of Human GAR Tfase: 10-(Trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic Acid Authors: Zhang, Y. / Desharnais, J. / Marsilje, T.H. / Li, C. / Hedrick, M.P. / Gooljarsingh, L.T. / Tavassoli, A. / Benkovic, S.J. / Olson, A.J. / Boger, D.L. / Wilson, I.A. | ||||||
History |
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Remark 600 | HETEROGEN The ligand has a trifluoroacetyl group when synthesized and is named 10-TRIFLUOROACETYL- ...HETEROGEN The ligand has a trifluoroacetyl group when synthesized and is named 10-TRIFLUOROACETYL-5,10-DIDEAZA-ACYCLIC-5,6,7,8- TETRAHYDROFOLIC ACID. When the compound interacts with protein human GAR Tfase, the ketone group is hydrolyzed to two hydroxyl groups ("gem-diol"). The hydrolyzed form was the binding form in the structure. The hydrolyzed compound is only stable when bound to enzyme. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171 KB | Display | ![]() |
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PDB format | ![]() | 136.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mejS 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
#1: Protein | Mass: 22678.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22102, phosphoribosylglycinamide formyltransferase 1 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.79 Å3/Da / Density % sol: 74.3 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, sitting drop Details: PEG4K, 0.2 Ammonium Sulfate, 50mM HEPES 6.7-7.0, VAPOR DIFFUSION, SITTING DROP, temperature 282K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / PH range low: 7 / PH range high: 6.7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2002 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→41.32 Å / Num. all: 60661 / Num. obs: 57912 / % possible obs: 95.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.88 % / Rsym value: 0.074 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 3.91 % / Mean I/σ(I) obs: 2.02 / Num. unique all: 2996 / Rsym value: 0.601 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 45 Å / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB code 1MEJ Resolution: 1.98→41.32 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.907 / SU B: 2.765 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.125 / Stereochemistry target values: Engh & Huber
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.295 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→41.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.981→2.033 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.227 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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