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Yorodumi- PDB-1cet: CHLOROQUINE BINDS IN THE COFACTOR BINDING SITE OF PLASMODIUM FALC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cet | ||||||
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Title | CHLOROQUINE BINDS IN THE COFACTOR BINDING SITE OF PLASMODIUM FALCIPARUM LACTATE DEHYDROGENASE. | ||||||
Components | PROTEIN (L-LACTATE DEHYDROGENASE) | ||||||
Keywords | OXIDOREDUCTASE / TRICARBOXYLIC ACID CYCLE / INHIBITOR | ||||||
Function / homology | Function and homology information L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Read, J.A. / Wilkinson, K.W. / Tranter, R. / Sessions, R.B. / Brady, R.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Chloroquine binds in the cofactor binding site of Plasmodium falciparum lactate dehydrogenase. Authors: Read, J.A. / Wilkinson, K.W. / Tranter, R. / Sessions, R.B. / Brady, R.L. #1: Journal: Nat.Struct.Biol. / Year: 1996 Title: The Structure of Lactate Dehydrogenase from Plasmodium Falciparum Reveals a New Target for Anti-Malarial Design Authors: Dunn, C.R. / Banfield, M.J. / Barker, J.J. / Higham, C.W. / Moreton, K.M. / Turgut-Balik, D. / Brady, R.L. / Holbrook, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cet.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cet.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cet.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cet_validation.pdf.gz | 694.9 KB | Display | wwPDB validaton report |
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Full document | 1cet_full_validation.pdf.gz | 697.1 KB | Display | |
Data in XML | 1cet_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 1cet_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/1cet ftp://data.pdbj.org/pub/pdb/validation_reports/ce/1cet | HTTPS FTP |
-Related structure data
Related structure data | 1ceqC 1ldgS S: Starting model for refinement C: citing same article (ref.) |
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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: 34162.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q27743, L-lactate dehydrogenase |
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#2: Chemical | ChemComp-CLQ / |
#3: 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: 2.3 Å3/Da / Density % sol: 40 % |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. obs: 20155 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LDG Resolution: 2.05→20 Å / Data cutoff high absF: 20 / Data cutoff low absF: 2.05 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 9.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 20115 / Num. reflection obs: 17783 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |