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- PDB-3nz9: Structural Analysis of Pneumocystis carinii and Human DHFR Comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nz9 | ||||||
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Title | Structural Analysis of Pneumocystis carinii and Human DHFR Complexes with NADPH and a Series of Five Potent 5-(omega-Carboxy(alkyloxy)Pyrido[2,3-d]pyrimidine Derivatives | ||||||
![]() | Dihydrofolate reductase | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / pneumocystis carinii DHFR inhibitor complexes / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cody, V. | ||||||
![]() | ![]() Title: Structural analysis of Pneumocystis carinii and human DHFR complexes with NADPH and a series of five potent 6-[5'-([omega]-carboxyalkoxy)benzyl]pyrido[2,3-d]pyrimidine derivatives Authors: Cody, V. / Pace, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.5 KB | Display | ![]() |
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PDB format | ![]() | 44.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 980.7 KB | Display | ![]() |
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Full document | ![]() | 990.2 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nz6C ![]() 3nzaC ![]() 3nzbC ![]() 3nzcC ![]() 3nzdC ![]() 3cd2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23918.537 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-D2K / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.69 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 33-336% PEG 2K, 46-52 mM MES pH 6 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 6, 2006 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 24011 / Num. obs: 22779 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.028 / Rsym value: 0.042 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 13.1 / Num. unique all: 2229 / Rsym value: 0.113 / % possible all: 90.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3cd2 Resolution: 1.8→24.51 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.895 / SU B: 3.22 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.167 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.375 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→24.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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