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Yorodumi- PDB-7lrk: Crystal structure of BPTF bromodomain in complex with inhibitor P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lrk | |||||||||
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Title | Crystal structure of BPTF bromodomain in complex with inhibitor Pdy-3-093 | |||||||||
Components | Nucleosome-remodeling factor subunit BPTF | |||||||||
Keywords | GENE REGULATION/INHIBITOR / BPTF / bromodomain / inhibitor / GENE REGULATION / GENE REGULATION-INHIBITOR complex | |||||||||
Function / homology | Function and homology information NURF complex / endoderm development / anterior/posterior pattern specification / embryonic placenta development / ATPase complex / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding ...NURF complex / endoderm development / anterior/posterior pattern specification / embryonic placenta development / ATPase complex / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / dendrite / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | |||||||||
Authors | Chan, A. / Schonbrunn, E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition. Authors: Zahid, H. / Buchholz, C.R. / Singh, M. / Ciccone, M.F. / Chan, A. / Nithianantham, S. / Shi, K. / Aihara, H. / Fischer, M. / Schonbrunn, E. / Dos Santos, C.O. / Landry, J.W. / Pomerantz, W.C.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lrk.cif.gz | 122 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lrk.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 7lrk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lrk_validation.pdf.gz | 976.3 KB | Display | wwPDB validaton report |
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Full document | 7lrk_full_validation.pdf.gz | 978.6 KB | Display | |
Data in XML | 7lrk_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 7lrk_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/7lrk ftp://data.pdbj.org/pub/pdb/validation_reports/lr/7lrk | HTTPS FTP |
-Related structure data
Related structure data | 7lp0C 7lpkC 7lroC 7rwnC 7rwoC 7rwpC 7rwqC 7k6rS C: citing same article (ref.) S: Starting model for refinement |
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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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14455.415 Da / Num. of mol.: 2 / Fragment: BPTF bromodomain (uniprot residues 2917-3037) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF, FAC1, FALZ / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12830 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: 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: 2.09 Å3/Da / Density % sol: 41.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5 and 25% polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→38.3 Å / Num. obs: 43465 / % possible obs: 98.3 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.071 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.44→1.48 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2851 / CC1/2: 0.876 / Rrim(I) all: 0.453 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7K6R Resolution: 1.44→38.28 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.5 Å2 / Biso mean: 11.8094 Å2 / Biso min: 3.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.44→38.28 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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