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Yorodumi- PDB-1klk: CRYSTAL STRUCTURE OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1klk | ||||||
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Title | CRYSTAL STRUCTURE OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE TERNARY COMPLEX WITH PT653 AND NADPH | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / Structure-based design / antifolate / AIDS / protein-inhibitor complex / NADP / One-carbon metabolism | ||||||
Function / homology | Function and homology information glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding Similarity search - Function | ||||||
Biological species | Pneumocystis carinii (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Rosowsky, A. / Queener, S.F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structure-based enzyme inhibitor design: modeling studies and crystal structure analysis of Pneumocystis carinii dihydrofolate reductase ternary complex with PT653 and NADPH. Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Rosowsky, A. / Queener, S.F. #1: Journal: Biochemistry / Year: 2000 Title: Structural Studies on Bioactive Compounds. 30. Crystal Structure and Molecular Modeling Studies on the Pneumocystis carinii Dihydrofolate Reductase Cofactor Complex with TAB, a Highly Selective Antifolate Authors: Cody, V. / Chan, D. / Galitsky, N. / Rak, D. / Luft, J.R. / Pangborn, W. / Queener, S.F. / Laughton, C.A. / Stevens, M.F.G. #2: Journal: Biochemistry / Year: 1999 Title: Ligand-Induced Conformational Changes in the Crystal Structure 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 | 1klk.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1klk.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 1klk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/1klk ftp://data.pdbj.org/pub/pdb/validation_reports/kl/1klk | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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) / Genus: Rattus / Organ: lung / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P16184, dihydrofolate reductase |
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#2: Chemical | ChemComp-PMD / [ |
#3: Chemical | ChemComp-NDP / |
#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: 1.96 Å3/Da / Density % sol: 37.32 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 Details: PEG 2000MME, KCl, MES, pH 6.0, VAPOR DIFFUSION, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / Method: batch method | |||||||||||||||||||||||||||||||||||
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: Oct 15, 1999 / 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: 2.3→25 Å / Num. all: 9597 / Num. obs: 5861 / % possible obs: 61.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 | ||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 23.4 / Num. unique all: 8889 / Rsym value: 0.234 / % possible all: 89.2 | ||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.073 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 44.4 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement | *PLUS Highest resolution: 2.4 Å / Num. reflection obs: 5802 / Num. reflection Rfree: 634 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |