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Yorodumi- PDB-1dg5: DIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLEXED W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dg5 | ||||||
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Title | DIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND TRIMETHOPRIM | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / DIHYDROFOLATE REDUCTASE / STRUCTURE-BASED INHIBITOR DESIGN / FOLATEANALOGS / ROSSMANN FOLD / NICOTINAMIDE ADENINE DINUCLEOTIDE / TRIMETHOPRIM / TUBERCULOSIS | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / NADP+ binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Li, R. / Sirawaraporn, R. / Chitnumsub, P. / Sirawaraporn, W. / Wooden, J. / Athappilly, F. / Turley, S. / Hol, W.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Three-dimensional structure of M. tuberculosis dihydrofolate reductase reveals opportunities for the design of novel tuberculosis drugs. Authors: Li, R. / Sirawaraporn, R. / Chitnumsub, P. / Sirawaraporn, W. / Wooden, J. / Athappilly, F. / Turley, S. / Hol, W.G. #1: Journal: Biochemistry / Year: 1997 Title: Comparison of Two Independent Crystal Structures of Human Dihydrofolate Reductase Ternary Complexes Reduced with Nicotinamide Adenine Dinucleotide Phosphate and the Very Tight-Binding Inhibitor PT523 Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Rosowsky, A. / Blakley, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dg5.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dg5.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/1dg5 ftp://data.pdbj.org/pub/pdb/validation_reports/dg/1dg5 | 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: 17660.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) References: UniProt: P0A546, UniProt: P9WNX1*PLUS, dihydrofolate reductase | ||
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#2: Chemical | ChemComp-NDP / | ||
#3: Chemical | ChemComp-TOP / | ||
#4: Chemical | #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: 3.1 Å3/Da / Density % sol: 60.36 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: AMMONIUM SULFATE, SODIUM ACETATE, GLYCEROL, NADPH, TRIMETHOPRIM, POTASSIUM PHOSPHATE, DTT, POTASSIUM CHLORIDE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0949 |
Detector | Type: SBC-2 / Detector: CCD / Date: Sep 17, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0949 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 14679 / % possible obs: 99.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.036 |
Reflection shell | Resolution: 2→2.09 Å / Rmerge(I) obs: 0.112 / % possible all: 98.3 |
Reflection shell | *PLUS % possible obs: 98.3 % / Mean I/σ(I) obs: 14 |
-Processing
Software |
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Refinement | Resolution: 2→50 Å / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.188 / Rfactor obs: 0.188 / σ(F): 1 / Stereochemistry target values: ENGH & HUBER | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 14677 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |