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Yorodumi- PDB-1u4s: Plasmodium falciparum lactate dehydrogenase complexed with 2,6-na... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u4s | ||||||
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Title | Plasmodium falciparum lactate dehydrogenase complexed with 2,6-naphthalenedisulphonic acid | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Conners, R. / Cameron, A. / Read, J. / 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. / 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 | 1u4s.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u4s.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 1u4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/1u4s ftp://data.pdbj.org/pub/pdb/validation_reports/u4/1u4s | HTTPS FTP |
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-Related structure data
Related structure data | 1u4oC 1u5aC 1u5cC 1xivC 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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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: 34846.387 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-BIH / |
#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: 2.4 Å3/Da / Density % sol: 48.41 % |
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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: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 14, 2001 / Details: Mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 19866 / Num. obs: 19866 / % possible obs: 90.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rsym value: 0.055 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2→2.15 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 3421 / Rsym value: 0.174 / % possible all: 79.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB model 1LDG Resolution: 2→29.36 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.141 / SU ML: 0.087 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.149 / ESU R Free: 0.142 / 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: 16.842 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.003→2.055 Å / Total num. of bins used: 20 /
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