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Open data
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Basic information
Entry | Database: PDB / ID: 2p5b | ||||||
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Title | The complex structure of JMJD2A and trimethylated H3K36 peptide | ||||||
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![]() | METAL BINDING PROTEIN / ![]() | ||||||
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 / response to nutrient levels / negative regulation of autophagy / HDMs demethylate histones / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, G. / Chen, Z. / Zang, J. / Hong, X. / Shi, Y. | ||||||
![]() | ![]() Title: Structural basis of the recognition of a methylated histone tail by JMJD2A. Authors: Chen, Z. / Zang, J. / Kappler, J. / Hong, X. / Crawford, F. / Wang, Q. / Lan, F. / Jiang, C. / Whetstine, J. / Dai, S. / Hansen, K. / Shi, Y. / Zhang, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.9 KB | Display | ![]() |
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PDB format | ![]() | 130.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABIJ
#1: Protein | Mass: 40863.504 Da / Num. of mol.: 2 / Fragment: catalytic core Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: O75164, ![]() #2: Protein/peptide | ![]() Mass: 2425.897 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: P84239 |
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-Non-polymers , 5 types, 293 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/OGA.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/OGA.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ![]() #6: Chemical | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.71 % |
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Crystal grow![]() | Method: evaporation / Details: EVAPORATION |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 52214 / Num. obs: 52214 / Biso Wilson estimate: 20.7 Å2 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.332 Å2 / ksol: 0.323 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.99→47.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.11 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
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Xplor file |
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