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Open data
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Basic information
Entry | Database: PDB / ID: 8f59 | ||||||
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Title | LSD1-CoREST in complex with AW2 and SNAG peptide | ||||||
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Function / homology | ![]() negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / negative regulation of vitamin D biosynthetic process / Regulation of CDH11 gene transcription / epithelial cell migration / epithelial to mesenchymal transition involved in endocardial cushion formation / trophoblast giant cell differentiation / positive regulation of megakaryocyte differentiation / guanine metabolic process ...negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / negative regulation of vitamin D biosynthetic process / Regulation of CDH11 gene transcription / epithelial cell migration / epithelial to mesenchymal transition involved in endocardial cushion formation / trophoblast giant cell differentiation / positive regulation of megakaryocyte differentiation / guanine metabolic process / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / Epithelial-Mesenchymal Transition (EMT) during gastrulation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caroli, J. / Mattevi, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Distal drug resistance mutations promote covalent inhibitor-adduct Grob fragmentation in LSD1 Authors: Caroli, J. / Mattevi, A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.5 KB | Display | ![]() |
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PDB format | ![]() | 136 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8bopC ![]() 8boxC ![]() 8f2zC ![]() 8f30C ![]() 8f6sC ![]() 8fdvC ![]() 2v1dS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 95051.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: O60341, [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase |
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#2: Protein | ![]() Mass: 16459.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Protein/peptide | ![]() Mass: 1102.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: Chemical | ChemComp-XB6 / [( Mass: 995.821 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H47N9O16P2 / Feature type: SUBJECT OF INVESTIGATION |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.65 Å3/Da / Density % sol: 78.22 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.2 Na/K Tartrate, 100 mM ADA pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→48.73 Å / Num. obs: 62710 / % possible obs: 99.7 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.043 / Rrim(I) all: 0.096 / Χ2: 0.99 / Net I/σ(I): 10.1 / Num. measured all: 277195 |
Reflection shell | Resolution: 2.8→2.87 Å / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 1.535 / Num. measured all: 19524 / Num. unique obs: 4567 / CC1/2: 0.309 / Rpim(I) all: 0.828 / Rrim(I) all: 1.754 / Χ2: 0.99 / Net I/σ(I) obs: 1.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2v1d Resolution: 2.8→48.73 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / 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: 2.8→48.73 Å
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Refine LS restraints |
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LS refinement shell |
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