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Yorodumi- PDB-6m61: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m61 | ||||||
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Title | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / heptelidic acid / Complex / OXIDOREDUCTASE PROTEIN | ||||||
Function / homology | Function and homology information 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 / NAD binding / microtubule cytoskeleton / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82449538629 Å | ||||||
Authors | Yan, Y. / Zang, X. / Cooper, S.J. / Lin, H. / Zhou, J. / Tang, Y. | ||||||
Citation | Journal: Chem Sci / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m61.cif.gz | 362 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m61.ent.gz | 233.3 KB | Display | PDB format |
PDBx/mmJSON format | 6m61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m61_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6m61_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6m61_validation.xml.gz | 61 KB | Display | |
Data in CIF | 6m61_validation.cif.gz | 89.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/6m61 ftp://data.pdbj.org/pub/pdb/validation_reports/m6/6m61 | HTTPS FTP |
-Related structure data
Related structure data | 6m5xC 1u8fS 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 OQPR
#1: Protein | Mass: 36246.340 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GAPDH, GAPD, CDABP0047, OK/SW-cl.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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