[English] 日本語
![](img/lk-miru.gif)
- PDB-1t25: Plasmodium falciparum lactate dehydrogenase complexed with NADH a... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1t25 | ||||||
---|---|---|---|---|---|---|---|
Title | Plasmodium falciparum lactate dehydrogenase complexed with NADH and 3-hydroxyisoxazole-4-carboxylic 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 | ![]() ![]() ![]() | ||||||
![]() | Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. ...Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. / Barros, D. / Lavandera, J.L. / Martin, J.J. / Risco, F. / Garcia-Ochoa, S. / Gamo, F.J. / Sanz, L. / Leon, L. / Ruiz, J.R. / Gabarro, R. / Mallo, A. / De Las Heras, F.G. | ||||||
![]() | ![]() Title: Identification and Activity of a Series of Azole-based Compounds with Lactate Dehydrogenase-directed Anti-malarial Activity. Authors: Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. / Barros, D. / Lavandera, J.L. / Martin, J.J. / ...Authors: Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. / Barros, D. / Lavandera, J.L. / Martin, J.J. / Risco, F. / Garcia-Ochoa, S. / Gamo, F.J. / Sanz, L. / Leon, L. / Ruiz, J.R. / Gabarro, R. / Mallo, A. / De Las Heras, F.G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 81.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 59.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1t24C ![]() 1t26C ![]() 1t2cC ![]() 1t2dC ![]() 1t2eC ![]() 1t2fC ![]() 1ldgS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: |
-
Components
#1: Protein | Mass: 34977.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: LDH / Plasmid: pKK223 / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-NAI / |
#3: Chemical | ChemComp-GAG / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 40 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.75 Å / Num. all: 26093 / Num. obs: 24119 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rsym value: 0.066 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.9→1.99 Å / Mean I/σ(I) obs: 4.7 / Rsym value: 0.227 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1LDG Resolution: 1.9→29.75 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.482 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 12.609 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|