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Yorodumi- PDB-5t4v: Crystal structure of the bromodomain of human BRPF1 in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t4v | ||||||
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Title | Crystal structure of the bromodomain of human BRPF1 in complex with NI-48 ligand | ||||||
Components | Peregrin | ||||||
Keywords | TRANSCRIPTION / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription ...acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Tallant, C. / Igoe, N. / Bayle, E.D. / Nunez-Alonso, G. / Newman, J.A. / Mathea, S. / Savitsky, P. / Fedorov, O. / Brennan, P.E. / Muller, S. ...Tallant, C. / Igoe, N. / Bayle, E.D. / Nunez-Alonso, G. / Newman, J.A. / Mathea, S. / Savitsky, P. / Fedorov, O. / Brennan, P.E. / Muller, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Fish, P. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Design of a Biased Potent Small Molecule Inhibitor of the Bromodomain and PHD Finger-Containing (BRPF) Proteins Suitable for Cellular and in Vivo Studies. Authors: Igoe, N. / Bayle, E.D. / Fedorov, O. / Tallant, C. / Savitsky, P. / Rogers, C. / Owen, D.R. / Deb, G. / Somervaille, T.C. / Andrews, D.M. / Jones, N. / Cheasty, A. / Ryder, H. / Brennan, P.E. ...Authors: Igoe, N. / Bayle, E.D. / Fedorov, O. / Tallant, C. / Savitsky, P. / Rogers, C. / Owen, D.R. / Deb, G. / Somervaille, T.C. / Andrews, D.M. / Jones, N. / Cheasty, A. / Ryder, H. / Brennan, P.E. / Muller, S. / Knapp, S. / Fish, P.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t4v.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t4v.ent.gz | 27 KB | Display | PDB format |
PDBx/mmJSON format | 5t4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t4v_validation.pdf.gz | 767 KB | Display | wwPDB validaton report |
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Full document | 5t4v_full_validation.pdf.gz | 767.5 KB | Display | |
Data in XML | 5t4v_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 5t4v_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/5t4v ftp://data.pdbj.org/pub/pdb/validation_reports/t4/5t4v | HTTPS FTP |
-Related structure data
Related structure data | 5t4uC 4lc2S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13703.698 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201 |
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#2: Chemical | ChemComp-N48 / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-FMT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.58 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 m bis-tris propane pH 8.5, 0.2 M sodium formate, 20% PEG 3350, 10% ethylene glycol PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→25.59 Å / Num. all: 17186 / Num. obs: 87628 / % possible obs: 99 % / Redundancy: 5.1 % / Biso Wilson estimate: 23.407 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rsym value: 0.034 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.65→1.67 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.897 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LC2 Resolution: 1.65→25.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.325 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.106 / 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: 35.233 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→25.59 Å
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Refine LS restraints |
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