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Yorodumi- PDB-4m5i: The Identification, Analysis and Structure-Based Development of N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m5i | ||||||
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Title | The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase | ||||||
Components | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / FOLATE BIOSYNTHESIS / Diphosphotransferases / PTERIN / ATP binding / Inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å | ||||||
Authors | Yun, M. / Hoagland, D. / Kumar, G. / Waddell, B. / Rock, C.O. / Lee, R.E. / White, S.W. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2014 Title: The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Authors: Yun, M.K. / Hoagland, D. / Kumar, G. / Waddell, M.B. / Rock, C.O. / Lee, R.E. / White, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m5i.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m5i.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 4m5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m5i_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4m5i_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4m5i_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 4m5i_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/4m5i ftp://data.pdbj.org/pub/pdb/validation_reports/m5/4m5i | HTTPS FTP |
-Related structure data
Related structure data | 4m5gSC 4m5hC 4m5jC 4m5kC 4m5lC 4m5mC 4m5nC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18380.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: folK, b0142, JW0138 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase |
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-Non-polymers , 5 types, 194 molecules
#2: Chemical | #3: Chemical | ChemComp-APC / | #4: Chemical | ChemComp-YH6 / | #5: Chemical | ChemComp-CL / | #6: 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: 1.97 Å3/Da / Density % sol: 37.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl, 0.2M calcium chloride, 25% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 17, 2013 / Details: Rosenbaum-Rock double-crystal monochromator |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→50 Å / Num. obs: 56757 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rsym value: 0.065 / Net I/σ(I): 33.2 |
Reflection shell | Resolution: 1.08→1.1 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 2431 / Rsym value: 0.316 / % possible all: 80.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PEB ENTRY 4M5G Resolution: 1.08→34.662 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.755 Å2 / ksol: 0.464 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.08→34.662 Å
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Refine LS restraints |
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LS refinement shell |
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