+Open data
-Basic information
Entry | Database: PDB / ID: 7tab | ||||||
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Title | G-925 bound to the SMARCA4 (BRG1) Bromodomain | ||||||
Components | Isoform 4 of Transcription activator BRG1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / bromodomain BRG1 SMARCA4 inhibitor / protein binding / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 2-(6-amino-5-phenylpyridazin-3-yl)phenol / Isoform 4 of Transcription activator BRG1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å | ||||||
Authors | Tang, Y. / Poy, F. / Taylor, A.M. / Cochran, A.G. / Bellon, S.F. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: GNE-064: A Potent, Selective, and Orally Bioavailable Chemical Probe for the Bromodomains of SMARCA2 and SMARCA4 and the Fifth Bromodomain of PBRM1. Authors: Taylor, A.M. / Bailey, C. / Belmont, L.D. / Campbell, R. / Cantone, N. / Cote, A. / Crawford, T.D. / Cummings, R. / DeMent, K. / Duplessis, M. / Flynn, M. / Good, A.C. / Huang, H.R. / Joshi, ...Authors: Taylor, A.M. / Bailey, C. / Belmont, L.D. / Campbell, R. / Cantone, N. / Cote, A. / Crawford, T.D. / Cummings, R. / DeMent, K. / Duplessis, M. / Flynn, M. / Good, A.C. / Huang, H.R. / Joshi, S. / Leblanc, Y. / Murray, J. / Nasveschuk, C.G. / Neiss, A. / Poy, F. / Romero, F.A. / Sandy, P. / Tang, Y. / Tsui, V. / Zawadzke, L. / Sims 3rd, R.J. / Audia, J.E. / Bellon, S.F. / Magnuson, S.R. / Albrecht, B.K. / Cochran, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tab.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tab.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 7tab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tab_validation.pdf.gz | 715.4 KB | Display | wwPDB validaton report |
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Full document | 7tab_full_validation.pdf.gz | 715.9 KB | Display | |
Data in XML | 7tab_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 7tab_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/7tab ftp://data.pdbj.org/pub/pdb/validation_reports/ta/7tab | HTTPS FTP |
-Related structure data
Related structure data | 7td9C 2grcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15104.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Production host: Escherichia coli (E. coli) References: UniProt: P51532-4, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#2: Chemical | ChemComp-GGU / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.74 % Description: Very thin plates that nonetheless diffract to extreme high resolution. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein in buffer: 20 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM TCEP, at a concentration of 15.55 mg/ml (1.03 mM) Reservoir solution contains: Jeffamine ED-2001 pH 7.0 at 30%, Tris-HCl pH 8.5 at 0.1 M, 4% PEG 400 PH range: 8.2-8.8 / Temp details: 4 degree Celsius |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: LN2 flow / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.98011 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.16→50 Å / Num. obs: 38722 / % possible obs: 98.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Χ2: 1.036 / Net I/σ(I): 8.6 / Num. measured all: 134810 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GRC Resolution: 1.16→32.88 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.434 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 42.28 Å2 / Biso mean: 13.091 Å2 / Biso min: 5.47 Å2
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Refinement step | Cycle: final / Resolution: 1.16→32.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.16→1.189 Å / Rfactor Rfree error: 0
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