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Open data
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Basic information
Entry | Database: PDB / ID: 6g2f | ||||||
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Title | X-ray structure of NSD3-PWWP1 in complex with compound 16 | ||||||
![]() | Histone-lysine N-methyltransferase NSD3 | ||||||
![]() | ONCOPROTEIN / Inhibitor / PWWP domain | ||||||
Function / homology | ![]() [histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / histone H3 methyltransferase activity / PKMTs methylate histone lysines / methylation ...[histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / histone H3 methyltransferase activity / PKMTs methylate histone lysines / methylation / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Boettcher, J. / Muellauer, B.J. / Weiss-Puxbaum, A. / Zoephel, A. | ||||||
![]() | ![]() Title: Fragment-based discovery of a chemical probe for the PWWP1 domain of NSD3. Authors: Bottcher, J. / Dilworth, D. / Reiser, U. / Neumuller, R.A. / Schleicher, M. / Petronczki, M. / Zeeb, M. / Mischerikow, N. / Allali-Hassani, A. / Szewczyk, M.M. / Li, F. / Kennedy, S. / ...Authors: Bottcher, J. / Dilworth, D. / Reiser, U. / Neumuller, R.A. / Schleicher, M. / Petronczki, M. / Zeeb, M. / Mischerikow, N. / Allali-Hassani, A. / Szewczyk, M.M. / Li, F. / Kennedy, S. / Vedadi, M. / Barsyte-Lovejoy, D. / Brown, P.J. / Huber, K.V.M. / Rogers, C.M. / Wells, C.I. / Fedorov, O. / Rumpel, K. / Zoephel, A. / Mayer, M. / Wunberg, T. / Bose, D. / Zahn, S. / Arnhof, H. / Berger, H. / Reiser, C. / Hormann, A. / Krammer, T. / Corcokovic, M. / Sharps, B. / Winkler, S. / Haring, D. / Cockcroft, X.L. / Fuchs, J.E. / Mullauer, B. / Weiss-Puxbaum, A. / Gerstberger, T. / Boehmelt, G. / Vakoc, C.R. / Arrowsmith, C.H. / Pearson, M. / McConnell, D.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.5 KB | Display | ![]() |
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PDB format | ![]() | 50.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 765.1 KB | Display | ![]() |
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Full document | ![]() | 765.2 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6g24C ![]() 6g25C ![]() 6g27C ![]() 6g29C ![]() 6g2bC ![]() 6g2cC ![]() 6g2eC ![]() 6g2oC ![]() 6g3pC ![]() 6g3tC 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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Unit cell |
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Components
#1: Protein | Mass: 16271.401 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9BZ95, histone-lysine N-methyltransferase |
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#2: Chemical | ChemComp-EHW / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.738→38.391 Å / Num. obs: 14431 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 31.15 Å2 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.738→1.768 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.743 / % possible all: 100 |
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Processing
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Refinement | Resolution: 1.74→38.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.103
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Displacement parameters | Biso max: 189.49 Å2 / Biso mean: 44.01 Å2 / Biso min: 20.41 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.74→38.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: -8.0081 Å / Origin y: 9.6079 Å / Origin z: -12.2353 Å
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Refinement TLS group | Selection details: { A|* } |