+Open data
-Basic information
Entry | Database: PDB / ID: 5a7q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human JMJD2A in complex with compound 30 | ||||||
Components | LYSINE-SPECIFIC DEMETHYLASE 4A | ||||||
Keywords | OXIDOREDUCTASE / JMJD2A / KDM4A | ||||||
Function / homology | Function and homology information [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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Velupillai, S. / Krojer, T. / Gileadi, C. / Johansson, C. / Korczynska, M. / Le, D.D. / Younger, N. / Gregori-Puigjane, E. / Tumber, A. / Iwasa, E. ...Velupillai, S. / Krojer, T. / Gileadi, C. / Johansson, C. / Korczynska, M. / Le, D.D. / Younger, N. / Gregori-Puigjane, E. / Tumber, A. / Iwasa, E. / Pollock, S.B. / Ortiz Torres, I. / Kopec, J. / Dixon-Clarke, S. / MacKenzie, A. / Nowak, R. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Shoichet, B.K. / Fujimori, D.G. / Oppermann, U. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors. Authors: Korczynska, M. / Le, D.D. / Younger, N. / Gregori-Puigjane, E. / Tumber, A. / Krojer, T. / Velupillai, S. / Gileadi, C. / Nowak, R.P. / Iwasa, E. / Pollock, S.B. / Ortiz Torres, I. / ...Authors: Korczynska, M. / Le, D.D. / Younger, N. / Gregori-Puigjane, E. / Tumber, A. / Krojer, T. / Velupillai, S. / Gileadi, C. / Nowak, R.P. / Iwasa, E. / Pollock, S.B. / Ortiz Torres, I. / Oppermann, U. / Shoichet, B.K. / Fujimori, D.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5a7q.cif.gz | 313.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5a7q.ent.gz | 254.9 KB | Display | PDB format |
PDBx/mmJSON format | 5a7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a7q_validation.pdf.gz | 470 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5a7q_full_validation.pdf.gz | 475 KB | Display | |
Data in XML | 5a7q_validation.xml.gz | 30 KB | Display | |
Data in CIF | 5a7q_validation.cif.gz | 42.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/5a7q ftp://data.pdbj.org/pub/pdb/validation_reports/a7/5a7q | HTTPS FTP |
-Related structure data
Related structure data | 5a7nC 5a7oC 5a7pC 5a7sC 5a7wC 5a80C 2oq7S C: citing same article (ref.) 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: UNP RESIDUES 1-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O75164, 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 |
---|
-Non-polymers , 6 types, 341 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: 28% PEG3350 -- 0.1M BIS-TRIS PH 6.5 -- 0.15M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→149.08 Å / Num. obs: 59779 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OQ7 Resolution: 2→83.7271 Å / σ(F): 2 / Stereochemistry target values: ML
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→83.7271 Å
|