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- PDB-7dyu: Human JMJD5 in complex with MN and 5-((4-phenylbutyl)amino)pyridi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dyu | ||||||
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Title | Human JMJD5 in complex with MN and 5-((4-phenylbutyl)amino)pyridine-2,4-dicarboxylic acid. | ||||||
![]() | Bifunctional peptidase and arginyl-hydroxylase JMJD5 | ||||||
![]() | OXIDOREDUCTASE / JmjC domain-containing protein 5 / JMJD5 / dioxygenase | ||||||
Function / homology | ![]() [protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle / p53 binding / chromosome / fibroblast proliferation / endopeptidase activity / in utero embryonic development / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / proteolysis / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakashima, Y. / Brewitz, L. / Schofield, C.J. | ||||||
![]() | ![]() Title: 5-Substituted Pyridine-2,4-dicarboxylate Derivatives Have Potential for Selective Inhibition of Human Jumonji-C Domain-Containing Protein 5. Authors: Brewitz, L. / Nakashima, Y. / Piasecka, S.K. / Salah, E. / Fletcher, S.C. / Tumber, A. / Corner, T.P. / Kennedy, T.J. / Fiorini, G. / Thalhammer, A. / Christensen, K.E. / Coleman, M.L. / Schofield, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.4 KB | Display | ![]() |
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PDB format | ![]() | 128.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7dytC ![]() 7dyvC ![]() 7dywC ![]() 7dyxC ![]() 6f4pS 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
#1: Protein | Mass: 27261.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8N371, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen ...References: UniProt: Q8N371, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor, Hydrolases; Acting on peptide bonds (peptidases) | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-MN / | #4: Chemical | ChemComp-HR9 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→49.86 Å / Num. obs: 38768 / % possible obs: 94.2 % / Redundancy: 12.4 % / Biso Wilson estimate: 22.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.155 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.72→1.85 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.805 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1040 / CC1/2: 0.351 / % possible all: 58.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6F4P Resolution: 1.72→49.86 Å / SU ML: 0.1264 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 22.1821 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→49.86 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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