+Open data
-Basic information
Entry | Database: PDB / ID: 6mv8 | |||||||||
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Title | LDHA structure in complex with inhibitor 14 | |||||||||
Components | L-lactate dehydrogenase A chain | |||||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / LDHA / inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | |||||||||
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 / SYNCHROTRON / Resolution: 1.95 Å | |||||||||
Authors | Eigenbrot, C.E. / Ultsch, M. / Wei, B. | |||||||||
Citation | Journal: To Be Published Title: Structure-based Optimization of Potent, Cell-Active Hydroxylactam Inhibitors of Lactate Dehydrogenase Authors: Wei, B. / Robarge, K. / Labadie, S.S. / Chen, J. / Corson, L.B. / DiPasquale, A. / Eigenbrot, C. / Ultsch, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mv8.cif.gz | 285.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mv8.ent.gz | 229.6 KB | Display | PDB format |
PDBx/mmJSON format | 6mv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mv8_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 6mv8_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 6mv8_validation.xml.gz | 56.8 KB | Display | |
Data in CIF | 6mv8_validation.cif.gz | 79.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/6mv8 ftp://data.pdbj.org/pub/pdb/validation_reports/mv/6mv8 | HTTPS FTP |
-Related 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) / Strain (production host): Rosetta 2 DE3 pLys S / References: UniProt: P00338, L-lactate dehydrogenase |
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-Non-polymers , 6 types, 736 molecules
#2: Chemical | ChemComp-NAI / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | ChemComp-LAC / | #7: 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: 2.2 Å3/Da / Density % sol: 44.05 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / Details: 30%PEG3350 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.947→38.651 Å / Num. all: 91115 / Num. obs: 91115 / % possible obs: 97.8 % / Redundancy: 3.4 % / Rpim(I) all: 0.029 / Rrim(I) all: 0.055 / Rsym value: 0.046 / Net I/av σ(I): 14.1 / Net I/σ(I): 16.6 / Num. measured all: 312212 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 1.95→50.01 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2012 / WRfactor Rwork: 0.1566 / FOM work R set: 0.8362 / SU B: 4.441 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1652 / SU Rfree: 0.1506 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 202.75 Å2 / Biso mean: 37.916 Å2 / Biso min: 16.19 Å2
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Refinement step | Cycle: final / Resolution: 1.95→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.055 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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