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Yorodumi- PDB-5w8i: Crystal Structure of Lactate Dehydrogenase A in complex with inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w8i | ||||||
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Title | Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 23 and Zinc | ||||||
Components | L-lactate dehydrogenase A chain | ||||||
Keywords | OXIDOREDUCTASE / oxidoreductase inhibitor | ||||||
Function / homology | Function and homology information oxidoreductase complex / L-lactate dehydrogenase / Pyruvate metabolism / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / Regulation of pyruvate metabolism / glycolytic process / cadherin binding ...oxidoreductase complex / L-lactate dehydrogenase / Pyruvate metabolism / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / Regulation of pyruvate metabolism / glycolytic process / cadherin binding / mitochondrion / extracellular exosome / identical protein binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.95 Å | ||||||
Authors | Lukacs, C.M. / Abendroth, J. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Discovery and Optimization of Potent, Cell-Active Pyrazole-Based Inhibitors of Lactate Dehydrogenase (LDH). Authors: Rai, G. / Brimacombe, K.R. / Mott, B.T. / Urban, D.J. / Hu, X. / Yang, S.M. / Lee, T.D. / Cheff, D.M. / Kouznetsova, J. / Benavides, G.A. / Pohida, K. / Kuenstner, E.J. / Luci, D.K. / ...Authors: Rai, G. / Brimacombe, K.R. / Mott, B.T. / Urban, D.J. / Hu, X. / Yang, S.M. / Lee, T.D. / Cheff, D.M. / Kouznetsova, J. / Benavides, G.A. / Pohida, K. / Kuenstner, E.J. / Luci, D.K. / Lukacs, C.M. / Davies, D.R. / Dranow, D.M. / Zhu, H. / Sulikowski, G. / Moore, W.J. / Stott, G.M. / Flint, A.J. / Hall, M.D. / Darley-Usmar, V.M. / Neckers, L.M. / Dang, C.V. / Waterson, A.G. / Simeonov, A. / Jadhav, A. / Maloney, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w8i.cif.gz | 513.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w8i.ent.gz | 420.7 KB | Display | PDB format |
PDBx/mmJSON format | 5w8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/5w8i ftp://data.pdbj.org/pub/pdb/validation_reports/w8/5w8i | HTTPS FTP |
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-Related structure data
Related structure data | 5w8hC 5w8jC 5w8kC 5w8lC 4jnkS 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 36734.672 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LDHA, PIG19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00338, L-lactate dehydrogenase |
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-Non-polymers , 7 types, 930 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-CIT / #5: Chemical | ChemComp-DMS / #6: Chemical | ChemComp-MLA / | #7: Chemical | ChemComp-GOL / | #8: 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: 2.34 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 6.8 Details: 24% PEG 3350, 200 mM Sodium Malonate, pH 6.8, 10% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 102092 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 26.99 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 21.84 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 3.2 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Starting model: IN-HOUSE APO SOLVED WITH MODEL 4JNK Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.974 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.126 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.62 Å2 / Biso mean: 21.13 Å2 / Biso min: 9.45 Å2
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Refinement step | Cycle: final / Resolution: 1.95→50 Å
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LS refinement shell | Resolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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