+Open data
-Basic information
Entry | Database: PDB / ID: 4aj2 | ||||||
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Title | rat LDHA in complex with 5-(2-chlorophenyl)-1H-tetrazole | ||||||
Components | L-LACTATE DEHYDROGENASE A CHAIN | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / OXIDOREDUCTASE-INHIBITOR COMPLEX / FRAGMENT-BASED LEAD GENERATED INHIBITORS | ||||||
Function / homology | Function and homology information 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 | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Tucker, J.A. / Brassington, C. / Hassall, G. / Vogtherr, M. / Ward, R. / Tart, J. / Davies, G. / Frazer, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aj2.cif.gz | 505 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aj2.ent.gz | 419 KB | Display | PDB format |
PDBx/mmJSON format | 4aj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aj2_validation.pdf.gz | 491.1 KB | Display | wwPDB validaton report |
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Full document | 4aj2_full_validation.pdf.gz | 503.5 KB | Display | |
Data in XML | 4aj2_validation.xml.gz | 58.5 KB | Display | |
Data in CIF | 4aj2_validation.cif.gz | 85.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/4aj2 ftp://data.pdbj.org/pub/pdb/validation_reports/aj/4aj2 | HTTPS FTP |
-Related structure data
Related structure data | 4aj1C 4aj4C 4ajeC 4ajhC 4ajiC 4ajjC 4ajkC 4ajlC 4ajnC 4ajoC 4ajpC 4al4C C: citing same article (ref.) |
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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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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.) RATTUS NORVEGICUS (Norway rat) / Tissue: MUSCLE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P04642, L-lactate dehydrogenase #2: Chemical | #3: Chemical | ChemComp-52C / #4: Chemical | ChemComp-MLI / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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