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- PDB-5o4s: Crystal structure of the human BRPF1 bromodomain in complex with BZ135 -

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Basic information

Entry
Database: PDB / ID: 5o4s
TitleCrystal structure of the human BRPF1 bromodomain in complex with BZ135
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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-9KW / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 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 30, 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
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4395
Polymers27,4072
Non-polymers1,0313
Water4,035224
1
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2503
Polymers13,7041
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1882
Polymers13,7041
Non-polymers4851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.700, 62.690, 48.820
Angle α, β, γ (deg.)90.00, 101.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 13703.698 Da / Num. of mol.: 2
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-9KW / ~{N}-[1,4-dimethyl-7-morpholin-4-yl-2,3-bis(oxidanylidene)quinoxalin-6-yl]-5,6,7,8-tetrahydronaphthalene-2-sulfonamide


Mass: 484.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H28N4O5S
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 297 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: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→38 Å / Num. obs: 29072 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.151 / Net I/σ(I): 22.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1578 / CC1/2: 0.961 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementStarting model: 4LC2

4lc2


Resolution: 1.75→38 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.36
RfactorNum. reflection% reflection
Rfree0.2207 2004 6.91 %
Rwork0.178 --
obs0.181 29017 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 72 224 2129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061964
X-RAY DIFFRACTIONf_angle_d0.7222663
X-RAY DIFFRACTIONf_dihedral_angle_d18.7511224
X-RAY DIFFRACTIONf_chiral_restr0.044280
X-RAY DIFFRACTIONf_plane_restr0.004394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.29771410.25451892X-RAY DIFFRACTION99
1.7938-1.84230.32991410.22911936X-RAY DIFFRACTION100
1.8423-1.89650.30161470.22281903X-RAY DIFFRACTION100
1.8965-1.95770.25431430.21211932X-RAY DIFFRACTION100
1.9577-2.02770.27091400.17441931X-RAY DIFFRACTION100
2.0277-2.10880.231350.16991903X-RAY DIFFRACTION100
2.1088-2.20480.20291430.17271931X-RAY DIFFRACTION100
2.2048-2.3210.2331450.17811937X-RAY DIFFRACTION100
2.321-2.46640.21571430.19131914X-RAY DIFFRACTION100
2.4664-2.65680.24811430.19791922X-RAY DIFFRACTION100
2.6568-2.92410.25121470.19571948X-RAY DIFFRACTION100
2.9241-3.3470.23971430.18171917X-RAY DIFFRACTION100
3.347-4.2160.1921510.15491956X-RAY DIFFRACTION100
4.216-38.01340.19531420.16881991X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 2.0436 Å / Origin y: 4.6943 Å / Origin z: 8.7135 Å
111213212223313233
T0.2399 Å2-0.0182 Å2-0.009 Å2-0.2318 Å20.0276 Å2--0.2396 Å2
L0.6721 °2-0.1478 °2-0.2445 °2-0.8266 °20.1795 °2--0.8053 °2
S-0.0175 Å °-0.0847 Å °0.0036 Å °0.0641 Å °0.0099 Å °-0.023 Å °0.0399 Å °-0.0222 Å °0 Å °
Refinement TLS groupSelection details: all

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