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- PDB-5o55: Crystal structure of the human BRPF1 bromodomain in complex with BZ047 -

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Basic information

Entry
Database: PDB / ID: 5o55
TitleCrystal structure of the human BRPF1 bromodomain in complex with BZ047
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
Chem-9L5 / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
DepositionMay 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 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 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1193
Polymers13,7041
Non-polymers4152
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint1 kcal/mol
Surface area7140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.695, 60.695, 63.147
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-987-

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 / Fragment: UNP residues 626-740
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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-9L5 / ~{N}-[(1~{S})-1-(1,5-dimethylpyrazol-4-yl)ethyl]-1-ethyl-3-methyl-2-oxidanylidene-quinoxaline-6-carboxamide


Mass: 353.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-tris propane, pH6.5, 0.15 M Sodium Nitrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999989 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 1.45→31.57 Å / Num. obs: 24259 / % possible obs: 99.8 % / Redundancy: 9.4 % / CC1/2: 1 / Rmerge(I) obs: 0.031 / Net I/σ(I): 31.2
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.468 / Num. unique obs: 3462 / CC1/2: 0.943 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 1.45→27.353 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.74
RfactorNum. reflection% reflection
Rfree0.2011 2005 8.27 %
Rwork0.1773 --
obs0.1793 24235 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→27.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 30 144 1109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081040
X-RAY DIFFRACTIONf_angle_d0.7551410
X-RAY DIFFRACTIONf_dihedral_angle_d11.7021103
X-RAY DIFFRACTIONf_chiral_restr0.062146
X-RAY DIFFRACTIONf_plane_restr0.004187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48630.28521410.24681538X-RAY DIFFRACTION97
1.4863-1.52640.22161390.20841544X-RAY DIFFRACTION100
1.5264-1.57140.21691440.19371587X-RAY DIFFRACTION100
1.5714-1.62210.21851380.18571570X-RAY DIFFRACTION100
1.6221-1.680.21791430.18621573X-RAY DIFFRACTION100
1.68-1.74730.21391430.18271575X-RAY DIFFRACTION100
1.7473-1.82680.2291420.18621594X-RAY DIFFRACTION100
1.8268-1.92310.20061380.18161560X-RAY DIFFRACTION100
1.9231-2.04350.22211440.18831591X-RAY DIFFRACTION100
2.0435-2.20130.18481430.17421579X-RAY DIFFRACTION100
2.2013-2.42270.21641430.17821616X-RAY DIFFRACTION100
2.4227-2.77290.21411410.18941598X-RAY DIFFRACTION100
2.7729-3.49250.20321510.17221623X-RAY DIFFRACTION100
3.4925-27.35760.18011550.16621682X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 15.2755 Å / Origin y: -22.5521 Å / Origin z: 0.4271 Å
111213212223313233
T0.1884 Å2-0.0809 Å2-0.0148 Å2-0.1969 Å20.0073 Å2--0.154 Å2
L2.1086 °2-1.1933 °20.9628 °2-3.478 °2-1.2402 °2--1.9893 °2
S0.0042 Å °-0.16 Å °-0.1218 Å °0.283 Å °-0.0291 Å °0.0654 Å °-0.0175 Å °-0.0944 Å °-0.0056 Å °
Refinement TLS groupSelection details: all

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