+Open data
-Basic information
Entry | Database: PDB / ID: 5uih | ||||||
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Title | structure of DHFR with bound phenformin and NADP | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / DHFR / phenformin / NADP | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.647 Å | ||||||
Authors | Pedersen, L.C. / London, R.E. | ||||||
Citation | Journal: Biochemistry / Year: 2017 Title: A Structural Basis for Biguanide Activity. Authors: Gabel, S.A. / Duff, M.R. / Pedersen, L.C. / DeRose, E.F. / Krahn, J.M. / Howell, E.E. / London, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uih.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uih.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 5uih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uih_validation.pdf.gz | 816 KB | Display | wwPDB validaton report |
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Full document | 5uih_full_validation.pdf.gz | 816.1 KB | Display | |
Data in XML | 5uih_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 5uih_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/5uih ftp://data.pdbj.org/pub/pdb/validation_reports/ui/5uih | HTTPS FTP |
-Related structure data
Related structure data | 5uiiC 5uioC 5uipC 1rc4S 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19076.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase |
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-Non-polymers , 6 types, 228 molecules
#2: Chemical | ChemComp-8CV / |
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#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-NAP / |
#5: Chemical | ChemComp-BME / |
#6: Chemical | ChemComp-EDO / |
#7: 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: 2.28 Å3/Da / Density % sol: 46.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 5mM phenformin, 1.15mM NADP,10mM trisodium citrate, 33% PEG 6K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Aug 25, 2015 / Details: varimaxHF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 20763 / % possible obs: 99.7 % / Redundancy: 5.9 % / Rsym value: 0.081 / Net I/av σ(I): 14.6 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.514 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RC4 Resolution: 1.647→23.339 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.647→23.339 Å
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Refine LS restraints |
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LS refinement shell |
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