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- PDB-6pg6: WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)but... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pg6 | ||||||
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Title | WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)acetamide | ||||||
![]() | WD repeat-containing protein 5 | ||||||
![]() | PROTEIN BINDING/Inhibitor / Inhibitor / Scaffolding Protein / B-propellor / Chromatin regulator / PROTEIN BINDING / 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 | ![]() | 145.4 KB | Display | ![]() |
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PDB format | ![]() | 112.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 933.9 KB | Display | ![]() |
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Full document | ![]() | 935.5 KB | Display | |
Data in XML | ![]() | 28.2 KB | Display | |
Data in CIF | ![]() | 42.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pg3SC ![]() 6pg4C ![]() 6pg5C ![]() 6pg7C ![]() 6pg8C ![]() 6pg9C ![]() 6pgaC ![]() 6pgbC ![]() 6pgcC ![]() 6pgdC ![]() 6pgeC ![]() 6pgfC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 31 - 334 / Label seq-ID: 11 - 314
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Components
#1: Protein | Mass: 34448.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 0.215 M ammonium sulfate, 0.1 M sodium cacodylate (pH 7.06), 25.6 %w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→43.74 Å / Num. obs: 70355 / % possible obs: 99 % / Redundancy: 7.4 % / CC1/2: 0.999 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3377 / CC1/2: 0.834 / % possible all: 94.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6PG3 Resolution: 1.68→43.74 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / 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: 17.336 Å2
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Refinement step | Cycle: 1 / Resolution: 1.68→43.74 Å
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Refine LS restraints |
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