+Open data
-Basic information
Entry | Database: PDB / ID: 7vd4 | ||||||
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Title | Crystal structure of BPTF-BRD with ligand TP248 bound | ||||||
Components | Nucleosome-remodeling factor subunit BPTF | ||||||
Keywords | ANTITUMOR PROTEIN / BPTF Bromodomain / Lysine acetylation / small-molecule inhibitor / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information NURF complex / methylated histone binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85659146555 Å | ||||||
Authors | Lu, T. / Lu, H.B. | ||||||
Funding support | 1items
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Citation | Journal: Bioorg.Chem. / Year: 2022 Title: Discovery of a highly potent CECR2 bromodomain inhibitor with 7H-pyrrolo[2,3-d] pyrimidine scaffold. Authors: Lu, H. / Lu, T. / Zu, S. / Duan, Z. / Guang, Y. / Li, Q. / Ma, J. / Chen, D. / Li, B. / Lu, W. / Jiang, H. / Luo, C. / Ye, D. / Chen, K. / Lin, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vd4.cif.gz | 47.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vd4.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 7vd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vd4_validation.pdf.gz | 735.5 KB | Display | wwPDB validaton report |
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Full document | 7vd4_full_validation.pdf.gz | 736.6 KB | Display | |
Data in XML | 7vd4_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 7vd4_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/7vd4 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/7vd4 | HTTPS FTP |
-Related structure data
Related structure data | 3qztS 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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Unit cell |
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-Components
#1: Protein | Mass: 13386.286 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF / Production host: Escherichia coli (E. coli) / References: UniProt: J3QQQ8 |
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#2: Chemical | ChemComp-6FI / |
#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: 2.16 Å3/Da / Density % sol: 43.14 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40 Å / Num. obs: 9679 / % possible obs: 96.37 % / Redundancy: 6 % / CC1/2: 0.897 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.05 / Rrim(I) all: 0.128 / Rsym value: 0.05 / Net I/σ(I): 97.7 |
Reflection shell | Resolution: 1.858→1.925 Å / Rmerge(I) obs: 0.456 / Num. unique obs: 840 / CC1/2: 0.89 / Rpim(I) all: 0.209 / Rrim(I) all: 0.512 / Rsym value: 0.209 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QZT Resolution: 1.85659146555→24.1139720626 Å / SU ML: 0.197206659844 / Cross valid method: NONE / σ(F): 1.36344065761 / Phase error: 37.5725600949 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 33.5877722999 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85659146555→24.1139720626 Å
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Refine LS restraints |
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LS refinement shell |
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