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- PDB-1u5a: Plasmodium falciparum lactate dehydrogenase complexed with 3,5-di... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1u5a | ||||||
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Title | Plasmodium falciparum lactate dehydrogenase complexed with 3,5-dihydroxy-2-naphthoic acid | ||||||
![]() | L-lactate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Protein-ligand complex | ||||||
Function / homology | ![]() L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Conners, R. / Cameron, A. / Read, J. / Schambach, F. / Sessions, R.B. / Brady, R.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.2 KB | Display | ![]() |
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PDB format | ![]() | 57.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.1 KB | Display | ![]() |
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Full document | ![]() | 441.4 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1u4oC ![]() 1u4sC ![]() 1u5cC ![]() 1xivC ![]() 1ldgS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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 |
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Components
#1: Protein | Mass: 34846.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Lactate dehydrogenase / Plasmid: pKK223 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-BIK / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.11 % |
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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: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 24, 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: 1.8→30 Å / Num. all: 29646 / Num. obs: 29208 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Rsym value: 0.059 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.8→1.94 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 5651 / Rsym value: 0.24 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDb entry 1LDG Resolution: 1.8→29.24 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.213 / SU ML: 0.067 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.105 / ESU R Free: 0.099 / 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: 13.749 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.845 Å / Total num. of bins used: 20
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