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Yorodumi- PDB-6pg9: WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)but... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pg9 | ||||||
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Title | WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)benzamide | ||||||
Components | WD repeat-containing protein 5 | ||||||
Keywords | PROTEIN BINDING/Inhibitor / Inhibitor / Scaffolding Protein / B-propellor / Chromatin regulator / PROTEIN BINDING / PROTEIN BINDING-Inhibitor complex | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Dennis, M.L. / Peat, T.S. | ||||||
Citation | Journal: Struct Dyn. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pg9.cif.gz | 141.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pg9.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 6pg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/6pg9 ftp://data.pdbj.org/pub/pdb/validation_reports/pg/6pg9 | HTTPS FTP |
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-Related structure data
Related structure data | 6pg3SC 6pg4C 6pg5C 6pg6C 6pg7C 6pg8C 6pgaC 6pgbC 6pgcC 6pgdC 6pgeC 6pgfC S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / 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: 0 / 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.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61964 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.31 Å3/Da / Density % sol: 46.78 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 0.182 M ammonium fluoride, 0.1 soidum cacodylate (pH 5.79), 22.1 %w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 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: 1.75→52.42 Å / Num. obs: 62036 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.97 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.75→1.79 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3516 / CC1/2: 0.781 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PG3 Resolution: 1.75→52.42 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.853 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.143 / 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: 12.722 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→52.42 Å
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Refine LS restraints |
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