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Yorodumi- PDB-5kkc: l-lactate dehydrogenase from rabbit muscle with the inhibitor 6DHNAD -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kkc | |||||||||||||||
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Title | l-lactate dehydrogenase from rabbit muscle with the inhibitor 6DHNAD | |||||||||||||||
Components | L-lactate dehydrogenase A chain | |||||||||||||||
Keywords | OXIDOREDUCTASE / lactate dehydrogenase / inhibitor / 6DHNAD / beta- 6-dihydronicotimide adenine dinucleotide | |||||||||||||||
Function / homology | Function and homology information L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.859 Å | |||||||||||||||
Authors | Meneely, K.M. / Moran, G.R. / Lamb, A.L. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2016 Title: Ligand binding phenomena that pertain to the metabolic function of renalase. Authors: Beaupre, B.A. / Roman, J.V. / Hoag, M.R. / Meneely, K.M. / Silvaggi, N.R. / Lamb, A.L. / Moran, G.R. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kkc.cif.gz | 493.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kkc.ent.gz | 413.1 KB | Display | PDB format |
PDBx/mmJSON format | 5kkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kkc_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5kkc_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5kkc_validation.xml.gz | 52.4 KB | Display | |
Data in CIF | 5kkc_validation.cif.gz | 73.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/5kkc ftp://data.pdbj.org/pub/pdb/validation_reports/kk/5kkc | HTTPS FTP |
-Related structure data
Related structure data | 5kkaC 5krqC 4i9hS S: Starting model for refinement 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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-Components
#1: Protein | Mass: 36467.352 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P13491, L-lactate dehydrogenase #2: Chemical | ChemComp-6V0 / [[( #3: Chemical | ChemComp-SO4 / #4: 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: 2.28 Å3/Da / Density % sol: 46.07 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Tris, pH 7.5, 0.08 M sodium acetate, 14% PEG 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 20, 2016 / Details: Rh coated flat, toroidal focusing |
Radiation | Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→39.41 Å / Num. obs: 108172 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.98 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.86→1.89 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I9H Resolution: 1.859→39.408 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.04 / Stereochemistry target values: ML
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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: 1.859→39.408 Å
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Refine LS restraints |
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LS refinement shell |
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