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Yorodumi- PDB-1c3e: NEW INSIGHTS INTO INHIBITOR DESIGN FROM THE CRYSTAL STRUCTURE AND... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c3e | ||||||
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Title | NEW INSIGHTS INTO INHIBITOR DESIGN FROM THE CRYSTAL STRUCTURE AND NMR STUDIES OF E. COLI GAR TRANSFORMYLATE IN COMPLEX WITH BETA-GAR AND 10-FORMYL-5,8,10-TRIDEAZAFOLIC ACID. | ||||||
Components | GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE | ||||||
Keywords | TRANSFERASE / PURINE BIOSYNTHESIS / ANTI-CANCER AGENT / INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process / DNA damage response / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Greasley, S.E. / Yamashita, M.M. / Cai, H. / Benkovic, S.J. / Boger, D.L. / Wilson, I.A. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: New insights into inhibitor design from the crystal structure and NMR studies of Escherichia coli GAR transformylase in complex with beta-GAR and 10-formyl-5,8,10-trideazafolic acid. Authors: Greasley, S.E. / Yamashita, M.M. / Cai, H. / Benkovic, S.J. / Boger, D.L. / Wilson, I.A. #1: Journal: J.Mol.Biol. / Year: 1998 Title: A pH Dependent Stabilization of an Active Site Loop Observed from Low and High pH Crystal Structures of Mutant Monomeric Glycinamide Ribonucleotide Transformylase at 1.8-1.9A Authors: Su, Y. / Yamashita, M.M. / Greasley, S.E. / Mullen, C.A. / Shim, J.H. / Jennings, P.A. / Benkovic, S.J. / Wilson, I.A. #2: Journal: Bioorg.Med.Chem. / Year: 1997 Title: 10-Formyl-5,8,10-trideazafolic acid (10-formyl-TDAF):a Potent Inhibitor of Glycinamide Ribonucleotide Transformylase. Authors: Boger, D.L. / Haynes, N.-E. / Kitos, P.A. / Ramcharan, J. / Marolewski, A.E. / Benkovic, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c3e.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c3e.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 1c3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c3e ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c3e | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22950.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURN / Production host: Escherichia coli (E. coli) References: UniProt: P08179, phosphoribosylglycinamide formyltransferase 1 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.92 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG 3350, Imidazole malate, calcium chloride, MPD, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 22.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 94 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 10, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 23742 / Num. obs: 23742 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.421 / Num. unique all: 2338 / % possible all: 99.3 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 99.3 % / Num. unique obs: 2338 / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Resolution: 2.1→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 471792.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 4.9 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.304 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.279 |