+Open data
-Basic information
Entry | Database: PDB / ID: 2w3m | ||||||
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Title | HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND FOLATE | ||||||
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 / dihydrofolate metabolic process / axon regeneration / folic acid binding / 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 / dihydrofolate metabolic process / axon regeneration / folic acid binding / G1/S-Specific Transcription / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / 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: 1.6 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 | 2w3m.cif.gz | 193.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w3m.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 2w3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/2w3m ftp://data.pdbj.org/pub/pdb/validation_reports/w3/2w3m | HTTPS FTP |
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-Related structure data
Related structure data | 2w3aC 2w3bC 2w3vC 2w3wC 1drfS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.066385, 0.997007, -0.039625), Vector: |
-Components
#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 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NDP): THE NADPH MAY BE A MIXTURE WITH ...NADPH DIHYDRO-NICOTINAMI | |
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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: 2.35 Å3/Da / Density % sol: 47.72 % / 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 (2 MM FINAL). CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION AT 277 K BY MIXING EQUAL VOLUMES OF PROTEIN/NADPH/FOLATE WITH RESERVOIR (24% ...Details: HUMAN DHFR/FOLATE COMPLEX WAS MIXED WITH NADPH (2 MM FINAL). CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION AT 277 K BY MIXING EQUAL VOLUMES OF PROTEIN/NADPH/FOLATE 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: 0.914 |
Detector | Type: ADSC QUANTUM-1 / Detector: CCD / Date: Jun 28, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.914 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→10.7 Å / Num. obs: 52618 / % possible obs: 98.4 % / Observed criterion σ(I): -10 / Redundancy: 5.6 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.8 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DRF Resolution: 1.6→10.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.7 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE OXIDATION STATE OF THE FOLATE LIGAND IS UNCLEAR FROM THE EXPERIMENTAL ELECTRON DENSITY MAPS. GIVEN THAT THE CRYSTAL WAS PREPARED WITH ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE OXIDATION STATE OF THE FOLATE LIGAND IS UNCLEAR FROM THE EXPERIMENTAL ELECTRON DENSITY MAPS. GIVEN THAT THE CRYSTAL WAS PREPARED WITH NADPH PRESENT, THE LIGAND MAY BE A MIXTURE OF FOLATE, 7,8-DIHYDROFOLATE, AND 5,6,7,8- TETRAHYDROFOLATE. IN ADDITION, THE OCCUPANCY ASSIGNED TO FOLATE, 0.8, WAS CHOSEN SO THAT THE AVERAGE TEMPERATURE FACTOR FOR THE PTERIDINE RING WAS SIMILAR TO SURROUNDING RESIDUES IN THE ACTIVE SITE. ACCORDINGLY, THE NADPH MAY BE A MIXTURE WITH THE OXIDIZED CO-FACTOR, NADP(+).
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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: 14.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→10.7 Å
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Refine LS restraints |
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