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Yorodumi- PDB-2w3a: HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND TRIMETHOPRIM -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w3a | ||||||
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Title | HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND TRIMETHOPRIM | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / NONCLASSICAL ANTIFOLATES / ONE-CARBON METABOLISM / LIPOPHILIC ANTIFOLATES / NADP / REDUCTASE | ||||||
Function / homology | Function and homology information regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / axon regeneration / folic acid binding / dihydrofolate metabolic process / G1/S-Specific Transcription ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / axon regeneration / folic acid binding / dihydrofolate metabolic process / G1/S-Specific Transcription / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity / 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: 1.5 Å | ||||||
Authors | Leung, A.K.W. / Reynolds, R.C. / Borhani, D.W. | ||||||
Citation | Journal: To be Published Title: Structural Basis for Selective Inhibition of Mycobacterium Avium Dihydrofolate Reductase by a Lipophilic Antifolate Authors: Leung, A.K.W. / Ross, L.J. / Zywno-Van Ginkel, S. / Reynolds, R.C. / Seitz, L.E. / Pathak, V. / Barrow, W.W. / White, E.L. / Suling, W.J. / Piper, J.R. / Borhani, D.W. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w3a.cif.gz | 185.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w3a.ent.gz | 149.5 KB | Display | PDB format |
PDBx/mmJSON format | 2w3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/2w3a ftp://data.pdbj.org/pub/pdb/validation_reports/w3/2w3a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.061704, 0.997265, -0.040674), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21480.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PDFR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00374, dihydrofolate reductase |
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-Non-polymers , 5 types, 415 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | GLYCEROL (GOL): 1,2,3-PROPANETRI |
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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: 2.34 Å3/Da / Density % sol: 47.47 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.75 Details: HUMAN DHFR/FOLATE COMPLEX WAS MIXED WITH NADPH AND TRIMETHOPRIM (BOTH 2 MM FINAL). CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION AT 277 K BY MIXING EQUAL VOLUMES OF PROTEIN/NADPH/TMP ...Details: HUMAN DHFR/FOLATE COMPLEX WAS MIXED WITH NADPH AND TRIMETHOPRIM (BOTH 2 MM FINAL). CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION AT 277 K BY MIXING EQUAL VOLUMES OF PROTEIN/NADPH/TMP WITH RESERVOIR (24% PEG 4000, 200 MM LI2SO4, 100 MM TRIS.HCL, PH 8.75). TRUNCATED TRIANGULAR CRYSTALS APPEARED SLOWLY, IN ABOUT A MONTH. THE CRYSTAL WAS CRYOPROTECTED WITH 15% GLYCEROL AND FLASH-COOLED IN LIQUID N2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: ADSC QUANTUM-1 / Detector: CCD / Date: Jul 14, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 55140 / % possible obs: 85.7 % / Observed criterion σ(I): -10 / Redundancy: 3.3 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2.9 / % possible all: 28.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED HUMAN DHFR FOLATE COMPLEX Resolution: 1.5→9.9 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.788 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.091 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.75 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→9.9 Å
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