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- PDB-5mwz: Crystal structure of the human BRPF1 bromodomain in complex with BZ073 -

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Basic information

Entry
Database: PDB / ID: 5mwz
TitleCrystal structure of the human BRPF1 bromodomain in complex with BZ073
ComponentsPeregrin
KeywordsDNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1(BRPF1) / monocytic leukemia zinc-finger (MOZ) / Inhibitor / transcription
Function / homology
Function and homology information


acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. ...BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å
AuthorsZhu, J. / Caflisch, A.
CitationJournal: Eur J Med Chem / Year: 2018
Title: Structure-based discovery of selective BRPF1 bromodomain inhibitors.
Authors: Zhu, J. / Zhou, C. / Caflisch, A.
History
DepositionJan 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1602
Polymers13,7041
Non-polymers4571
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.811, 60.811, 63.207
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1007-

HOH

21A-1022-

HOH

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Components

#1: Protein Peregrin / Bromodomain and PHD finger-containing protein 1 / Protein Br140


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
#2: Chemical ChemComp-KGU / ~{N}-[1,4-diethyl-2,3-bis(oxidanylidene)-7-piperidin-1-yl-quinoxalin-6-yl]-2-(4-methylpiperazin-1-yl)ethanamide


Mass: 456.581 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H36N6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris Propane pH7.4, 25% PEG3350, 5% EG, 0.15 M NaNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000019 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000019 Å / Relative weight: 1
ReflectionResolution: 1.25→40.46 Å / Num. obs: 37830 / % possible obs: 99.9 % / Redundancy: 18.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.014 / Net I/σ(I): 31.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 1.25→40.46 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.73
RfactorNum. reflection% reflection
Rfree0.1807 2010 5.32 %
Rwork0.1638 --
obs0.1647 37798 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.25→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 33 228 1203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041014
X-RAY DIFFRACTIONf_angle_d0.7681373
X-RAY DIFFRACTIONf_dihedral_angle_d11.065656
X-RAY DIFFRACTIONf_chiral_restr0.066143
X-RAY DIFFRACTIONf_plane_restr0.006178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.28130.18691420.1652520X-RAY DIFFRACTION100
1.2813-1.31590.17291450.16692519X-RAY DIFFRACTION100
1.3159-1.35470.16311420.1642532X-RAY DIFFRACTION100
1.3547-1.39840.18841440.16622503X-RAY DIFFRACTION100
1.3984-1.44840.16921460.16492545X-RAY DIFFRACTION100
1.4484-1.50640.16241410.15522539X-RAY DIFFRACTION100
1.5064-1.57490.1811390.15072543X-RAY DIFFRACTION100
1.5749-1.65790.18321440.15422542X-RAY DIFFRACTION100
1.6579-1.76180.19461350.15562543X-RAY DIFFRACTION100
1.7618-1.89790.19151450.16522552X-RAY DIFFRACTION100
1.8979-2.08880.20011420.15812576X-RAY DIFFRACTION100
2.0888-2.39110.16531470.16162561X-RAY DIFFRACTION100
2.3911-3.01230.19591470.17342613X-RAY DIFFRACTION100
3.0123-40.48140.17421510.16612700X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -14.8917 Å / Origin y: 23.3194 Å / Origin z: 0.8872 Å
111213212223313233
T0.0874 Å2-0.0148 Å20.0057 Å2-0.0783 Å2-0.0026 Å2--0.0772 Å2
L0.6106 °2-0.1821 °2-0.2947 °2-0.941 °20.4598 °2--0.637 °2
S0.0178 Å °-0.0361 Å °0.0658 Å °0.0302 Å °0.0006 Å °-0.0659 Å °-0.0295 Å °0.0346 Å °0.0006 Å °
Refinement TLS groupSelection details: all

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