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Yorodumi- PDB-1ly4: Analysis of quinazoline and PYRIDO[2,3D]PYRIMIDINE N9-C10 reverse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ly4 | ||||||
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Title | Analysis of quinazoline and PYRIDO[2,3D]PYRIMIDINE N9-C10 reversed bridge antifolates in complex with NADP+ and Pneumocystis carinii dihydrofolate reductase | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / pcDHFR / N9-C10 reversed bridge pyridopyrimidine antifolate | ||||||
Function / homology | Function and homology information 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 | Pneumocystis carinii (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Queener, S.F. / Gangjee, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Analysis of quinazoline and pyrido[2,3-d]pyrimidine N9-C10 reversed-bridge antifolates in complex with NADP+ and Pneumocystis carinii dihydrofolate reductase. Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Queener, S.F. / Gangjee, A. #1: Journal: Structure / Year: 1994 Title: The structure of Pneumocystis carinii dihydrofolate reductase to 1.9 A resolution Authors: Champness, J.N. / Achari, A. / Ballantine, S.P. / Bryant, P.K. / Delves, C.J. / Stammers, D.K. #2: Journal: Biochemistry / Year: 1999 Title: Ligand-induced conformational changes in the crystal structures of Pneumocystis carinii dihydrofolate reductase complexes with folate and NADP+ Authors: Cody, V. / Galitsky, N. / Rak, D. / Luft, J.R. / Pangborn, W. / Queener, S.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ly4.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ly4.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ly4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ly4_validation.pdf.gz | 972.1 KB | Display | wwPDB validaton report |
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Full document | 1ly4_full_validation.pdf.gz | 1011.4 KB | Display | |
Data in XML | 1ly4_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 1ly4_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/1ly4 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/1ly4 | HTTPS FTP |
-Related structure data
Related structure data | 1ly3C 1cd2S 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
#1: Protein | Mass: 23918.537 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pneumocystis carinii (fungus) / Plasmid: pEt11b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21c / References: UniProt: P16184, dihydrofolate reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-COQ / |
#4: 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: 2.02 Å3/Da / Density % sol: 39.16 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 Details: MES/KCl, PEG 2000, pH 6.0, VAPOR DIFFUSION, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: unknown | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K | ||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418,1.5621,1.7321 | ||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 9, 1998 / Details: mirrors | ||||||||||||
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→8 Å / Num. all: 10692 / Num. obs: 8544 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.2 Å2 | ||||||||||||
Reflection shell | Resolution: 2→2.1 Å / % possible all: 69.1 | ||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.066 | ||||||||||||
Reflection shell | *PLUS % possible obs: 69.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CD2 Resolution: 2.1→8 Å / σ(F): 2 / σ(I): 2 /
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Displacement parameters | Biso mean: 30.2 Å2 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.1 Å | ||||||||||||
Refinement | *PLUS Num. reflection all: 10692 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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