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- PDB-6pgf: WDR5delta32 bound to N-(4-(4-(hydroxymethyl)-1H-imidazol-2-yl)but... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pgf | ||||||
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Title | WDR5delta32 bound to N-(4-(4-(hydroxymethyl)-1H-imidazol-2-yl)butyl)acrylamide | ||||||
![]() | WD repeat-containing protein 5 | ||||||
![]() | PROTEIN BINDING/INHIBITOR / Inhibitor / Scaffolding Protein / B-propellor / Chromatin regulator / PROTEIN BINDING-INHIBITOR complex | ||||||
Function / homology | ![]() MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dennis, M.L. / Peat, T.S. | ||||||
![]() | ![]() Title: Fragment screening for a protein-protein interaction inhibitor to WDR5. Authors: Dennis, M.L. / Morrow, B.J. / Dolezal, O. / Cuzzupe, A.N. / Stupple, A.E. / Newman, J. / Bentley, J. / Hattarki, M. / Nuttall, S.D. / Foitzik, R.C. / Street, I.P. / Stupple, P.A. / Monahan, B.J. / Peat, T.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84 KB | Display | ![]() |
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PDB format | ![]() | 60.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 681.6 KB | Display | ![]() |
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Full document | ![]() | 682 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pg3C ![]() 6pg4SC ![]() 6pg5C ![]() 6pg6C ![]() 6pg7C ![]() 6pg8C ![]() 6pg9C ![]() 6pgaC ![]() 6pgbC ![]() 6pgcC ![]() 6pgdC ![]() 6pgeC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33537.016 Da / Num. of mol.: 1 / Fragment: UNP residues 32-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-OJP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.45 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 0.16 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 6.1, 30.1% w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→48.71 Å / Num. obs: 43339 / % possible obs: 97.1 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.54→1.57 Å / Redundancy: 12 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1913 / CC1/2: 0.847 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6PG4 Resolution: 1.54→48.71 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.177 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.07 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.526 Å2
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Refinement step | Cycle: 1 / Resolution: 1.54→48.71 Å
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Refine LS restraints |
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