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Yorodumi- PDB-5fjh: Crystal structure of human JMJD2C catalytic domain in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 5fjh | ||||||
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Title | Crystal structure of human JMJD2C catalytic domain in complex with epitherapuetic compound 2-(((2-((2-(dimethylamino)ethyl) (ethyl)amino) -2-oxoethyl)amino)methyl)isonicotinic acid | ||||||
Components | LYSINE-SPECIFIC DEMETHYLASE 4C | ||||||
Keywords | OXIDOREDUCTASE / TRANSCRIPTION REGULATION / METAL BINDING / DEMETHYLASE / LYSINE-SPECIFIC DEMETHYLASE 4C | ||||||
Function / homology | Function and homology information H3K9me3 modified histone binding / histone H3K36 demethylase activity / regulation of stem cell differentiation / blastocyst formation / regulation of androgen receptor signaling pathway / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / nuclear androgen receptor binding / stem cell population maintenance / androgen receptor signaling pathway ...H3K9me3 modified histone binding / histone H3K36 demethylase activity / regulation of stem cell differentiation / blastocyst formation / regulation of androgen receptor signaling pathway / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / nuclear androgen receptor binding / stem cell population maintenance / androgen receptor signaling pathway / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / nuclear receptor coactivator activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / regulation of gene expression / chromatin remodeling / positive regulation of cell population proliferation / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cecatiello, V. / Pasqualato, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structures of Human Jmjd2C Catalytic Domain Bound to Inhibitors Authors: Cecatiello, V. / Pasqualato, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fjh.cif.gz | 298.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fjh.ent.gz | 243.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fjh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fjh_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5fjh_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5fjh_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 5fjh_validation.cif.gz | 47.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/5fjh ftp://data.pdbj.org/pub/pdb/validation_reports/fj/5fjh | HTTPS FTP |
-Related structure data
Related structure data | 5fjkC 2xmlS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (1, -0.001466, 0.000877), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40517.246 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 3-347 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: Q9H3R0, 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 , 6 types, 541 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.6 % / Description: NONE |
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Crystal grow | pH: 7.25 Details: 21% PEG 3350 5% 1,2-ETHANEDIOL 0.2 M NANO3 0.1 M BIS-TRIS PROPANE PH 7.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→54.77 Å / Num. obs: 50575 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 23.42 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XML Resolution: 2.1→54.767 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 26.52 / 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: 2.1→54.767 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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