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- PDB-6dfr: CRYSTAL STRUCTURES OF ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dfr | ||||||
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Title | CRYSTAL STRUCTURES OF ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. THE NADP+ HOLOENZYME AND THE FOLATE(DOT)NADP+ TERNARY COMPLEX. SUBSTRATE BINDING AND A MODEL FOR THE TRANSITION STATE | ||||||
![]() | DIHYDROFOLATE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / OXIDO-REDUCTASE | ||||||
Function / homology | ![]() methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Bystroff, C. / Oatley, S.J. / Kraut, J. | ||||||
![]() | ![]() Title: Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state. Authors: Bystroff, C. / Oatley, S.J. / Kraut, J. #1: ![]() Title: Crystal Structure of Unliganded Escherichia Coli Dihydrofolate Reductase. Ligand-Induced Conformational Changes and Cooperativity in Binding Authors: Bystroff, C. / Kraut, J. #2: ![]() Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. I. General Features and Binding of Methotrexate Authors: Bolin, J.T. / Filman, D.J. / Matthews, D.A. / Hamlin, R.C. / Kraut, J. #3: ![]() Title: Effect of Single Amino Acid Replacements on the Folding and Stability of Dihydrofolate Reductase from Escherichia Coli Authors: Perry, K.M. / Onuffer, J.J. / Touchette, N.A. / Herndon, C.S. / Gittelman, M.S. / Matthews, C.R. / Chen, J.-T. / Mayer, R.J. / Taira, K. / Benkovic, S.J. / Howell, E.E. / Kraut, J. #4: ![]() Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. II. Environment of Bound Nadph and Implications for Catalysis Authors: Filman, D.J. / Bolin, J.T. / Matthews, D.A. / Kraut, J. #5: ![]() Title: Crystal Structure of Avian Dihydrofolate Reductase Containing Phenyltriazine and Nadph Authors: Volz, K.W. / Matthews, D.A. / Alden, R.A. / Freer, S.T. / Hansch, C. / Kaufman, B.T. / Kraut, J. #6: ![]() Title: Interpretation of Nuclear Magnetic Resonance Spectra for Lactobacillus Casei Dihydrofolate Reductase Based on the X-Ray Structure of the Enzyme-Methotrexate-Nadph Complex Authors: Matthews, D.A. #7: ![]() Title: Dihydrofolate Reductase from Lactobacillus Casei. Stereochemistry of Nadph Binding Authors: Matthews, D.A. / Alden, R.A. / Freer, S.T. / Xuong, N.-H. / Kraut, J. #8: ![]() Title: Proton Magnetic Resonance Studies on Escherichia Coli Dihydrofolate Reductase. Assignment of Histidine C-2 Protons in Binary Complexes with Folates on the Basis of the Crystal Structure with ...Title: Proton Magnetic Resonance Studies on Escherichia Coli Dihydrofolate Reductase. Assignment of Histidine C-2 Protons in Binary Complexes with Folates on the Basis of the Crystal Structure with Methotrexate and on Chemical Modifications Authors: Poe, M. / Hoogsteen, K. / Matthews, D.A. #9: ![]() Title: Dihydrofolate Reductase from Lactobacillus Casei. X-Ray Structure of the Enzyme-Methotrexate-Nadph Complex Authors: Matthews, D.A. / Alden, R.A. / Bolin, J.T. / Filman, D.J. / Freer, S.T. / Hamlin, R. / Hol, W.G.J. / Kisliuk, R.L. / Pastore, E.J. / Plante, L.T. / Xuong, N.-H. / Kraut, J. #10: ![]() Title: Dihydrofolate Reductase. The Amino Acid Sequence of the Enzyme from a Methotrexate-Resistant Mutant of Escherichia Coli Authors: Bennett, C.D. / Rodkey, J.A. / Sondey, J.M. / Hirschmann, R. #11: ![]() Title: Dihydrofolate Reductase. X-Ray Structure of the Binary Complex with Methotrexate Authors: Matthews, D.A. / Alden, R.A. / Bolin, J.T. / Freer, S.T. / Hamlin, R. / Xuong, N. / Kraut, J. / Poe, M. / Williams, M. / Hoogsteen, K. #12: ![]() Title: Dihydrofolate Reductase. Purification and Characterization of the Enzyme from an Amethopterin-Resistant Mutant of Escherichia Coli Authors: Poe, M. / Greenfield, N.J. / Hirshfield, J.M. / Williams, M.N. / Hoogsteen, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.2 KB | Display | ![]() |
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PDB format | ![]() | 33.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: THE PEPTIDE BOND LINKING GLY 95 TO GLY 96 IS IN THE CIS CONFORMATION. |
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Components
#1: Protein | Mass: 18020.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-NAP / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | THE NMN MOIETY OF NADP+ APPEARS TO BE DISORDERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.93 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.33 Å / Num. obs: 7586 / % possible obs: 99.5 % / Num. measured all: 41396 / Rmerge(I) obs: 0.047 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.192 / Highest resolution: 2.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.4 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.4 Å / Rfactor obs: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23 Å2 |