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- PDB-2h2q: Crystal structure of Trypanosoma cruzi Dihydrofolate Reductase-Th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2h2q | ||||||
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Title | Crystal structure of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate synthase | ||||||
![]() | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
![]() | OXIDOREDUCTASE / TRANSFERASE / Bifunctional enzyme in complex with NADP and dUMP | ||||||
Function / homology | ![]() thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Senkovich, O. / Schormann, N. / Chattopadhyay, D. | ||||||
![]() | ![]() Title: Structure-based approach to pharmacophore identification, in silico screening, and three-dimensional quantitative structure-activity relationship studies for inhibitors of Trypanosoma cruzi ...Title: Structure-based approach to pharmacophore identification, in silico screening, and three-dimensional quantitative structure-activity relationship studies for inhibitors of Trypanosoma cruzi dihydrofolate reductase function. Authors: Schormann, N. / Senkovich, O. / Walker, K. / Wright, D.L. / Anderson, A.C. / Rosowsky, A. / Ananthan, S. / Shinkre, B. / Velu, S. / Chattopadhyay, D. | ||||||
History |
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Remark 999 | SEQUENCE Authors state that the difference in sequence could arise due to PCR mutation, ...SEQUENCE Authors state that the difference in sequence could arise due to PCR mutation, polymorphism of DHFR-TS or error in database sequence |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 217.8 KB | Display | ![]() |
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PDB format | ![]() | 172.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 40.8 KB | Display | |
Data in CIF | ![]() | 56.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cl9C ![]() 3clbC ![]() 1j3iS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4 / Auth seq-ID: 2 - 515 / Label seq-ID: 2 - 515
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Components
#1: Protein | Mass: 58904.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q27793, dihydrofolate reductase, thymidylate synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.65 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 17% 2-Methyl-2,4-Pentanediol, 10% PEG 4000, 0.1M Potassium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 2, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 45396 / Num. obs: 45818 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.061 / Χ2: 0.628 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.24 / Num. unique all: 4372 / Χ2: 0.514 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1J3I Resolution: 2.4→43.15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.92 / SU B: 16.021 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.541 / ESU R Free: 0.269 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→43.15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3930 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.452 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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