+Open data
-Basic information
Entry | Database: PDB / ID: 6iq6 | ||||||
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Title | Crystal structure of GAPDH | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase | ||||||
Keywords | HYDROLASE / GAPDH / Inhibitor / Complex | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Park, J.B. / Park, H.Y. | ||||||
Citation | Journal: Mol.Cells / Year: 2019 Title: Structural Study of Monomethyl Fumarate-Bound Human GAPDH. Authors: Park, J.B. / Park, H. / Son, J. / Ha, S.J. / Cho, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iq6.cif.gz | 488.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iq6.ent.gz | 407.8 KB | Display | PDB format |
PDBx/mmJSON format | 6iq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iq6_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6iq6_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6iq6_validation.xml.gz | 88.7 KB | Display | |
Data in CIF | 6iq6_validation.cif.gz | 119 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/6iq6 ftp://data.pdbj.org/pub/pdb/validation_reports/iq/6iq6 | HTTPS FTP |
-Related structure data
Related structure data | 4wncS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36099.168 Da / Num. of mol.: 8 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-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups #2: Chemical | ChemComp-AW9 / ( #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: 2.35 Å3/Da / Density % sol: 47.68 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium Acetate, 0.1 M HEPES-NaOH pH 7.5, 22 % (w/v) PEG 4000, 4.4 % (v/v) Formamide |
-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 270 / Detector: CCD / Date: Jul 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→40.52 Å / Num. obs: 114488 / % possible obs: 99.74 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.29→2.33 Å / Rmerge(I) obs: 0.358 / Num. unique obs: 24713 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WNC Resolution: 2.29→35.87 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.505 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.25 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 33.081 Å2
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Refinement step | Cycle: 1 / Resolution: 2.29→35.87 Å
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