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Yorodumi- PDB-1ddr: MOLECULE: DIHYDROFOLATE REDUCTASE (E.C.1.5.1.3) COMPLEXED WITH ME... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ddr | ||||||
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Title | MOLECULE: DIHYDROFOLATE REDUCTASE (E.C.1.5.1.3) COMPLEXED WITH METHOTREXATE AND UREA | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / OXIDO-REDUCTASE | ||||||
Function / homology | Function and homology information methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.45 Å | ||||||
Authors | Yennawar, H.P. / Farber, G.K. | ||||||
Citation | Journal: Protein Sci. / Year: 1997 Title: The effect of denaturants on protein structure. Authors: Dunbar, J. / Yennawar, H.P. / Banerjee, S. / Luo, J. / Farber, G.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ddr.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ddr.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ddr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1ddr ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1ddr | 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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Atom site foot note | 1: GLY A 95 - GLY A 96 OMEGA = 359.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: GLY B 95 - GLY B 96 OMEGA = 1.14 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18019.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: B / References: UniProt: P0ABQ4, dihydrofolate reductase |
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-Non-polymers , 5 types, 189 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-URE / #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.1 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.54 |
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Detector | Type: RIGAKU AFC-6R / Detector: DIFFRACTOMETER / Date: Jan 11, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 15448 / % possible obs: 100 % / Redundancy: 1 % / Rmerge(I) obs: 0.11 |
Reflection | *PLUS Num. obs: 6948 / Observed criterion σ(F): 2 / Num. measured all: 18640 / Rmerge(I) obs: 0.11 |
-Processing
Software |
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Refinement | Resolution: 2.45→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.157 / Rfactor Rfree: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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