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- PDB-6m61: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor h... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m61 | ||||||
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Title | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid | ||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / heptelidic acid / Complex / OXIDOREDUCTASE PROTEIN | ||||||
Function / homology | ![]() peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / aspartic-type endopeptidase inhibitor activity / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / GAIT complex ...peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / aspartic-type endopeptidase inhibitor activity / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / GAIT complex / Glycolysis / positive regulation of type I interferon production / regulation of macroautophagy / defense response to fungus / lipid droplet / positive regulation of cytokine production / glycolytic process / cellular response to type II interferon / microtubule cytoskeleton organization / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose metabolic process / microtubule cytoskeleton / NAD binding / disordered domain specific binding / NADP binding / microtubule binding / nuclear membrane / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / vesicle / killing of cells of another organism / protein stabilization / negative regulation of translation / ribonucleoprotein complex / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yan, Y. / Zang, X. / Cooper, S.J. / Lin, H. / Zhou, J. / Tang, Y. | ||||||
![]() | ![]() Title: Biosynthesis of the fungal glyceraldehyde-3-phosphate dehydrogenase inhibitor heptelidic acid and mechanism of self-resistance Authors: Yan, Y. / Zang, X. / Cooper, S.J. / Lin, H. / Zhou, J. / Tang, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 362 KB | Display | ![]() |
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PDB format | ![]() | 233.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 61 KB | Display | |
Data in CIF | ![]() | 89.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m5xC ![]() 1u8fS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules OQPR
#1: Protein | Mass: 36246.340 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups |
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-Non-polymers , 7 types, 1173 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/F4F.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/F4F.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-ZN / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.97 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M zinc acetate dihydrate, 0.1 M Sodium acetate trihydrate, pH 4.6, 12% w/v polyethylene glycol (PEG) 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. obs: 142957 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 19.228006632 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.83→1.86 Å / Rmerge(I) obs: 0.866 / Num. unique obs: 142957 / CC1/2: 0.751 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1U8F Resolution: 1.82449538629→43.0321686884 Å / SU ML: 0.217157103773 / Cross valid method: FREE R-VALUE / σ(F): 1.33786284913 / Phase error: 22.4024440202
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5209129398 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82449538629→43.0321686884 Å
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Refine LS restraints |
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LS refinement shell |
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