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- PDB-5fpv: Crystal structure of human JMJD2A in complex with compound KDOAM20A -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fpv | ||||||
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Title | Crystal structure of human JMJD2A in complex with compound KDOAM20A | ||||||
![]() | LYSINE-SPECIFIC DEMETHYLASE 4A | ||||||
![]() | OXIDOREDUCTASE / JMJD2A / KDM4A | ||||||
Function / homology | ![]() [histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / negative regulation of autophagy / response to nutrient levels / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Srikannathasan, V. / Gileadi, C. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | ||||||
![]() | ![]() Title: Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development. Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, ...Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, A. / Steuber, H. / Egner, U. / Badock, V. / Munro, S. / Lathangue, N.B. / Westaway, S. / Brown, J. / Athanasou, N. / Prinjha, R. / Brennan, P.E. / Oppermann, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 912 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 108 KB | Display | |
Data in CIF | ![]() | 141.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uf0C ![]() 5a1fC ![]() 5a3pC ![]() 5a3tC ![]() 5a3wC ![]() 5fpuC ![]() 5funC ![]() 5fupC ![]() 5fv3C ![]() 5fwjC ![]() 4uraS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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8 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 41854.617 Da / Num. of mol.: 8 / Fragment: RESIDUES 4-354 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O75164, [histone H3]-dimethyl-L-lysine36 demethylase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one ...References: UniProt: O75164, [histone H3]-dimethyl-L-lysine36 demethylase, 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 |
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-Non-polymers , 5 types, 930 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/MMK.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MMK.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-MMK / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-NI / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.75 % / Description: NONE |
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Crystal grow | pH: 5.9 Details: 0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2014 / Details: MIRRORS |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→106.83 Å / Num. obs: 438854 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 35.69 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.44→2.57 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4URA Resolution: 2.44→85.327 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 25.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.44→85.327 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 67.1046 Å / Origin y: 16.421 Å / Origin z: 39.3987 Å
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Refinement TLS group | Selection details: ALL |