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- PDB-5o5a: Crystal structure of the human BRPF1 bromodomain in complex with BZ032 -

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Basic information

Entry
Database: PDB / ID: 5o5a
TitleCrystal structure of the human BRPF1 bromodomain in complex with BZ032
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 / zinc ion binding / nucleoplasm / nucleus / 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, PHD-type, conserved site / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain 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-9LN / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionJun 1, 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)14,1693
Polymers13,7041
Non-polymers4652
Water1,65792
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint2 kcal/mol
Surface area6990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.693, 60.693, 63.044
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-956-

HOH

21A-990-

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-NO3 / NITRATE ION


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


Mass: 403.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 49.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-tris propane, pH6.5, 0.2 M Sodium nitrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.6→40.37 Å / Num. obs: 18144 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 25.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 900 / CC1/2: 0.879 / % possible all: 100

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Processing

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

4lc2


Resolution: 1.6→40.37 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.31
RfactorNum. reflection% reflection
Rfree0.2016 1813 10.01 %
Rwork0.1778 --
obs0.1802 18115 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→40.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 34 92 1063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011031
X-RAY DIFFRACTIONf_angle_d0.8861397
X-RAY DIFFRACTIONf_dihedral_angle_d11.478874
X-RAY DIFFRACTIONf_chiral_restr0.052144
X-RAY DIFFRACTIONf_plane_restr0.005185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6003-1.64360.23591390.21121251X-RAY DIFFRACTION99
1.6436-1.69190.24941370.20951217X-RAY DIFFRACTION100
1.6919-1.74650.2161380.19781245X-RAY DIFFRACTION100
1.7465-1.8090.21681330.18491220X-RAY DIFFRACTION100
1.809-1.88140.22661330.18491237X-RAY DIFFRACTION100
1.8814-1.9670.23971350.1951257X-RAY DIFFRACTION100
1.967-2.07070.2181390.1791244X-RAY DIFFRACTION100
2.0707-2.20040.20051410.17341239X-RAY DIFFRACTION100
2.2004-2.37030.21791450.18141252X-RAY DIFFRACTION99
2.3703-2.60880.21631370.1851258X-RAY DIFFRACTION100
2.6088-2.98620.23471390.20121267X-RAY DIFFRACTION100
2.9862-3.76190.20871450.1731288X-RAY DIFFRACTION100
3.7619-40.3840.16471520.16251327X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 15.1456 Å / Origin y: -22.6901 Å / Origin z: 0.7362 Å
111213212223313233
T0.2225 Å2-0.0782 Å2-0.0443 Å2-0.2344 Å20.0218 Å2--0.2006 Å2
L1.7785 °2-0.5284 °20.8707 °2-3.3685 °2-1.0235 °2--1.9058 °2
S0.1091 Å °-0.1953 Å °-0.1632 Å °0.2343 Å °-0.1355 Å °0.1124 Å °-0.0194 Å °-0.0717 Å °0.0011 Å °
Refinement TLS groupSelection details: all

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