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- PDB-8fdz: Human GAR transformylase in complex with GAR substrate and AGF302... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fdz | |||||||||
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Title | Human GAR transformylase in complex with GAR substrate and AGF302 inhibitor | |||||||||
![]() | Phosphoribosylglycinamide formyltransferase | |||||||||
![]() | LIGASE / GARFTase / purine biosynthesis / monomer | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Wong-Roushar, J. / Dann III, C.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Multitargeted 6-Substituted Thieno[2,3- d ]pyrimidines as Folate Receptor-Selective Anticancer Agents that Inhibit Cytosolic and Mitochondrial One-Carbon Metabolism. Authors: Tong, N. / Wong-Roushar, J. / Wallace-Povirk, A. / Shah, Y. / Nyman, M.C. / Katinas, J.M. / Schneider, M. / O'Connor, C. / Bao, X. / Kim, S. / Li, J. / Hou, Z. / Matherly, L.H. / Dann 3rd, C.E. / Gangjee, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.5 KB | Display | ![]() |
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PDB format | ![]() | 38.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8fdxC ![]() 8fdyC ![]() 8fe0C ![]() 5j9fS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 22810.139 Da / Num. of mol.: 1 / Fragment: GART domain Source method: isolated from a genetically manipulated source Details: a / Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P22102 |
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#2: Chemical | ChemComp-GAR / |
#3: Chemical | ChemComp-XSO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Tris-HCl pH 7.5, 0.33 M NaCl, 16-21% PEG 4000, and 2% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jun 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→39.55 Å / Num. obs: 11949 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.992 / Rpim(I) all: 0.087 / Rrim(I) all: 0.276 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.48→2.58 Å / Num. unique obs: 1317 / CC1/2: 0.365 / Rpim(I) all: 0.85 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5J9F Resolution: 2.48→39.55 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.48→39.55 Å
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Refine LS restraints |
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LS refinement shell |
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