+
Open data
-
Basic information
Entry | Database: PDB / ID: 5fyi | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human JMJD2A in complex with pyruvate | ||||||
![]() | LYSINE-SPECIFIC DEMETHYLASE 4A | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() histone H3-tri/dimethyl-lysine-36 demethylase activity / [histone H3]-trimethyl-L-lysine36 demethylase / histone demethylation / histone H3-K36 demethylation / histone H3-methyl-lysine-36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3-tri/dimethyl-lysine-9 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / negative regulation of histone H3-K9 trimethylation / histone H3-K9 demethylation ...histone H3-tri/dimethyl-lysine-36 demethylase activity / [histone H3]-trimethyl-L-lysine36 demethylase / histone demethylation / histone H3-K36 demethylation / histone H3-methyl-lysine-36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3-tri/dimethyl-lysine-9 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / negative regulation of histone H3-K9 trimethylation / histone H3-K9 demethylation / histone H3-methyl-lysine-9 demethylase activity / negative regulation of astrocyte differentiation / pericentric heterochromatin / histone demethylase activity / negative regulation of cell death / negative regulation of autophagy / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / response to nutrient levels / HDMs demethylate histones / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nowak, R. / Kopec, J. / Johansson, C. / Szykowska, A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | ||||||
![]() | ![]() Title: Crystal Structure of Human Jmjd2A in Complex with Pyruvate Authors: Nowak, R. / Kopec, J. / Johansson, C. / Szykowska, A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 160.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 130.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 359.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 372.4 KB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a7oS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: RESIDUES 4-354 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: O75164, ![]() |
---|
-Non-polymers , 7 types, 353 molecules 












#2: Chemical | ![]() #3: Chemical | ChemComp-PYR / ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-EDO / ![]() #6: Chemical | #7: Chemical | ChemComp-1KA / ( | #8: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.44 % / Description: NONE |
---|---|
Crystal grow![]() | pH: 6 Details: 0.1M BIS-TRIS PH 6.0 -- 0.2M AMMONIUM SULFATE -- 28% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→29.77 Å / Num. obs: 51046 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.3 / % possible all: 99.2 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 5A7O Resolution: 2.096→29.767 Å / σ(F): 1.34 / Stereochemistry target values: ML / Details: DISORDERED SIDE-CHAINS WERE REMOVED.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.096→29.767 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|