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Open data
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Basic information
Entry | Database: PDB / ID: 4aj2 | ||||||
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Title | rat LDHA in complex with 5-(2-chlorophenyl)-1H-tetrazole | ||||||
![]() | L-LACTATE DEHYDROGENASE A CHAIN | ||||||
![]() | OXIDOREDUCTASE/INHIBITOR / OXIDOREDUCTASE-INHIBITOR COMPLEX / FRAGMENT-BASED LEAD GENERATED INHIBITORS | ||||||
Function / homology | ![]() lactate dehydrogenase activity / Pyruvate metabolism / sperm fibrous sheath / pyruvate catabolic process / oxidoreductase complex / : / L-lactate dehydrogenase / NAD metabolic process / lactate metabolic process / L-lactate dehydrogenase activity ...lactate dehydrogenase activity / Pyruvate metabolism / sperm fibrous sheath / pyruvate catabolic process / oxidoreductase complex / : / L-lactate dehydrogenase / NAD metabolic process / lactate metabolic process / L-lactate dehydrogenase activity / glucose catabolic process to lactate via pyruvate / pyruvate metabolic process / response to glucose / skeletal muscle tissue development / response to cAMP / response to nutrient / liver development / response to hydrogen peroxide / response to organic cyclic compound / kinase binding / response to estrogen / NAD binding / response to hypoxia / response to xenobiotic stimulus / positive regulation of apoptotic process / mitochondrion / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tucker, J.A. / Brassington, C. / Hassall, G. / Vogtherr, M. / Ward, R. / Tart, J. / Davies, G. / Frazer, M. | ||||||
![]() | ![]() Title: The Design and Synthesis of Novel Lactate Dehydrogenase a Inhibitors by Fragment-Based Lead Generation Authors: Ward, R. / Brassington, C. / Breeze, A.L. / Caputo, A. / Critchlow, S. / Davies, G. / Goodwin, L. / Hassall, G. / Greenwood, R. / Holdgate, G. / Mrosek, M. / Norman, R.A. / Pearson, S. / ...Authors: Ward, R. / Brassington, C. / Breeze, A.L. / Caputo, A. / Critchlow, S. / Davies, G. / Goodwin, L. / Hassall, G. / Greenwood, R. / Holdgate, G. / Mrosek, M. / Norman, R.A. / Pearson, S. / Tart, J. / Tucker, J.A. / Vogtherr, M. / Whittaker, D. / Wingfield, J. / Winter, J. / Hudson, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 505 KB | Display | ![]() |
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PDB format | ![]() | 419 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.1 KB | Display | ![]() |
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Full document | ![]() | 503.5 KB | Display | |
Data in XML | ![]() | 58.5 KB | Display | |
Data in CIF | ![]() | 85.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aj1C ![]() 4aj4C ![]() 4ajeC ![]() 4ajhC ![]() 4ajiC ![]() 4ajjC ![]() 4ajkC ![]() 4ajlC ![]() 4ajnC ![]() 4ajoC ![]() 4ajpC ![]() 4al4C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 36363.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-52C / #4: Chemical | ChemComp-MLI / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 1.5M NA MALONATE PH 7.0, 2% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 8, 2008 / Details: VARIMAXHF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→68.9 Å / Num. obs: 91637 / % possible obs: 71.5 % / Observed criterion σ(I): 2 / Redundancy: 3.27 % / Biso Wilson estimate: 16.596 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.75→1.82 Å / Redundancy: 1.39 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.1 / % possible all: 9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: INTERNAL RAT LDHA STRUCTURE Resolution: 1.75→49.21 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.491 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE-CHAINS HAVE BEEN TRUNCATED. DIFFERENCE DENSITY CONSISTENT WITH AN ADDITIONAL BINDING SITE FOR TETRAZOLE LIGAND VISIBLE AT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE-CHAINS HAVE BEEN TRUNCATED. DIFFERENCE DENSITY CONSISTENT WITH AN ADDITIONAL BINDING SITE FOR TETRAZOLE LIGAND VISIBLE AT SYMMETRY CONTACT, HOWEVER, NOT CLEAR ENOUGH TO BE MODELLED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.584 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→49.21 Å
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Refine LS restraints |
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