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Yorodumi- PDB-1xiv: Plasmodium falciparum lactate dehydrogenase complexed with 2-({4-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xiv | ||||||
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Title | Plasmodium falciparum lactate dehydrogenase complexed with 2-({4-chloro-[hydroxy(methoxy)methyl]cyclohexyl}amino)ethane-1,1,2-triol | ||||||
Components | L-lactate dehydrogenaseLactate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Protein-ligand complex | ||||||
Function / homology | Function and homology information L-lactate dehydrogenase / L-lactate dehydrogenase activity / carboxylic acid metabolic process Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Conners, R. / Cameron, A. / Read, J.A. / Schambach, F. / Sessions, R.B. / Brady, R.L. | ||||||
Citation | Journal: MOL.BIOCHEM.PARASITOL. / Year: 2005 Title: Mapping the binding site for gossypol-like inhibitors of Plasmodium falciparum lactate dehydrogenase Authors: Conners, R. / Schambach, F. / Read, J.A. / Cameron, A. / Sessions, R.B. / Vivas, L. / Easton, A. / Croft, S.L. / Brady, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xiv.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xiv.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/1xiv ftp://data.pdbj.org/pub/pdb/validation_reports/xi/1xiv | HTTPS FTP |
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-Related structure data
Related structure data | 1u4oC 1u4sC 1u5aC 1u5cC 1ldgS 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 on special symmetry positions |
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Details | The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the following operations and lattice translations: x,-y,-z/1,0,0 -x,y,-z/0,1,0 -x,-y,z/1,1,0 |
-Components
#1: Protein | Mass: 35055.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Plasmid: pKK223 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q27743, L-lactate dehydrogenase |
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#2: Chemical | ChemComp-RB2 / |
#3: Chemical | ChemComp-GOL / |
#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: 2.41 Å3/Da / Density % sol: 48.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 21, 2001 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 35317 / Num. obs: 33657 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rsym value: 0.058 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.7→1.78 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 4018 / Rsym value: 0.207 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LDG Resolution: 1.7→29.36 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.639 / SU ML: 0.055 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.092 / ESU R Free: 0.093 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.233 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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