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- PDB-8jdq: Crystal structure of H405A mLDHD in complex with D-2-hydroxyisoca... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jdq | |||||||||
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Title | Crystal structure of H405A mLDHD in complex with D-2-hydroxyisocaproic acid | |||||||||
![]() | Probable D-lactate dehydrogenase, mitochondrial | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Jin, S. / Chen, X. / Yang, J. / Ding, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Lactate dehydrogenase D is a general dehydrogenase for D-2-hydroxyacids and is associated with D-lactic acidosis. Authors: Jin, S. / Chen, X. / Yang, J. / Ding, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114 KB | Display | ![]() |
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PDB format | ![]() | 83.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8jdbC ![]() 8jdcC ![]() 8jddC ![]() 8jdeC ![]() 8jdfC ![]() 8jdgC ![]() 8jdnC ![]() 8jdoC ![]() 8jdpC ![]() 8jdrC ![]() 8jdsC ![]() 8jdtC ![]() 8jduC ![]() 8jdvC ![]() 8jdxC ![]() 8jdyC ![]() 8jdzC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 50385.789 Da / Num. of mol.: 1 / Mutation: H405A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q7TNG8, ![]() |
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#2: Chemical | ChemComp-FAD / ![]() |
#3: Chemical | ChemComp-2RH / ( |
#4: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.67 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion / Details: 4.0 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.39→31.91 Å / Num. obs: 97883 / % possible obs: 94.9 % / Redundancy: 11.6 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.012 / Rrim(I) all: 0.041 / Χ2: 0.92 / Net I/σ(I): 28.4 / Num. measured all: 1137949 |
Reflection shell | Resolution: 1.39→1.43 Å / % possible obs: 68.3 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.824 / Num. measured all: 29537 / Num. unique obs: 5175 / CC1/2: 0.657 / Rpim(I) all: 0.365 / Rrim(I) all: 0.908 / Χ2: 0.76 / Net I/σ(I) obs: 1.7 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→30.62 Å
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Refine LS restraints |
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LS refinement shell |
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