+Open data
-Basic information
Entry | Database: PDB / ID: 3ghw | ||||||
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Title | Human dihydrofolate reductase inhibitor complex | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / human dihydrofoalte reductase inhibitor complex / NADP / One-carbon metabolism | ||||||
Function / homology | Function and homology information regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | ||||||
Authors | Cody, V. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Design, synthesis, and X-ray crystal structure of classical and nonclassical 2-amino-4-oxo-5-substituted-6-ethylthieno[2,3-d]pyrimidines as dual thymidylate synthase and dihydrofolate ...Title: Design, synthesis, and X-ray crystal structure of classical and nonclassical 2-amino-4-oxo-5-substituted-6-ethylthieno[2,3-d]pyrimidines as dual thymidylate synthase and dihydrofolate reductase inhibitors and as potential antitumor agents Authors: Gangjee, A. / Li, W. / Kisliuk, R.L. / Cody, V. / Pace, J. / Piraino, J. / Makin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ghw.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ghw.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ghw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/3ghw ftp://data.pdbj.org/pub/pdb/validation_reports/gh/3ghw | HTTPS FTP |
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-Related structure data
Related structure data | 3ghcC 3ghvC 3gi2C 1u72S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 21349.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR, DHFRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00374, dihydrofolate reductase |
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#2: Chemical | ChemComp-GHW / |
#3: Chemical | ChemComp-NDP / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.21 % |
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Crystal grow | Temperature: 298 K / pH: 6.9 Details: 100 mM KPO4, pH 6.9, 30% AmSO4, 3& v/v ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9422 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 8, 2008 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9422 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→42.33 Å / Num. obs: 59523 / % possible obs: 82.7 % / Observed criterion σ(I): 1 / Redundancy: 9.9 % / Biso Wilson estimate: 12.24 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.036 |
Reflection shell | Resolution: 1.03→1.09 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.042 / Mean I/σ(I) obs: 0.32 / Rsym value: 0.023 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U72 Resolution: 1.24→22.17 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.695 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.144 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.24→22.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.24→1.27 Å / Total num. of bins used: 20
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