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Yorodumi- PDB-8fdy: Human GAR transformylase in complex with GAR substrate and AGF132... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fdy | |||||||||
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Title | Human GAR transformylase in complex with GAR substrate and AGF132 inhibitor | |||||||||
Components | Phosphoribosylglycinamide formyltransferase | |||||||||
Keywords | TRANSFERASE / GARFTas / purine biosynthesis / monomer | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | |||||||||
Authors | Wong-Roushar, J. / Dann III, C.E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Pharmacol Transl Sci / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fdy.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fdy.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 8fdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/8fdy ftp://data.pdbj.org/pub/pdb/validation_reports/fd/8fdy | HTTPS FTP |
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-Related structure data
Related structure data | 8fdxC 8fdzC 8fe0C 5j9fS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GART, PGFT, PRGS Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P22102, phosphoribosylglycinamide formyltransferase 1 |
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#2: Chemical | ChemComp-GAR / |
#3: Chemical | ChemComp-XSI / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.4 % |
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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: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Dec 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→39.7558 Å / Num. obs: 20659 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 0.997 / Rpim(I) all: 0.064 / Rrim(I) all: 0.209 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.06→2.12 Å / Num. unique obs: 1578 / CC1/2: 0.383 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J9F Resolution: 2.06→39.7558 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.36 / 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: 2.06→39.7558 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -31.8136 Å / Origin y: 18.8203 Å / Origin z: 27.9284 Å
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Refinement TLS group | Selection details: all |