+Open data
-Basic information
Entry | Database: PDB / ID: 5zjf | ||||||
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Title | LDHA-MA | ||||||
Components | L-lactate dehydrogenase A chain | ||||||
Keywords | OXIDOREDUCTASE / LDHA / inhibitor / machilin a | ||||||
Function / homology | Function and homology information oxidoreductase complex / Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion ...oxidoreductase complex / Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å | ||||||
Authors | Han, C.W. / Jang, S.B. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Cancers (Basel) / Year: 2019 Title: Machilin A Inhibits Tumor Growth and Macrophage M2 Polarization Through the Reduction of Lactic Acid. Authors: Chung, T.-W. / Kim, E.-Y. / Han, C.W. / Park, S.Y. / Jeong, M.S. / Yoon, D. / Choi, H.-J. / Jin, L. / Park, M.-J. / Kwon, Y.J. / Lee, H. / Kim, K.-J. / Park, K.H. / Kim, S. / Jang, S.B. / Ha, K.-T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zjf.cif.gz | 743.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zjf.ent.gz | 621.1 KB | Display | PDB format |
PDBx/mmJSON format | 5zjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zjf_validation.pdf.gz | 962.3 KB | Display | wwPDB validaton report |
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Full document | 5zjf_full_validation.pdf.gz | 1015.8 KB | Display | |
Data in XML | 5zjf_validation.xml.gz | 133.8 KB | Display | |
Data in CIF | 5zjf_validation.cif.gz | 184.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/5zjf ftp://data.pdbj.org/pub/pdb/validation_reports/zj/5zjf | HTTPS FTP |
-Related structure data
Related structure data | 5zjdC 5zjeC 4oknS 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 37432.355 Da / Num. of mol.: 12 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 #2: Chemical | ChemComp-9G9 / | #3: 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: 2.92 Å3/Da / Density % sol: 57.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 8% Tacsimate (pH 7.0), 20% Polyethylene glycol (PEG) 3350 PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→37.1 Å / Num. obs: 153798 / % possible obs: 99.4 % / Redundancy: 1 % / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.6→2.63 Å / Num. unique obs: 560845 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OKN Resolution: 2.602→37.1 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.602→37.1 Å
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Refine LS restraints |
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LS refinement shell |
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