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- PDB-6ekq: Crystal structure of the human BRPF1 bromodomain complexed with B... -

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Basic information

Entry
Database: PDB / ID: 6ekq
TitleCrystal structure of the human BRPF1 bromodomain complexed with BZ054 in space group C2
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-B0H / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionSep 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Assembly

Deposited unit
A: Peregrin
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2286
Polymers27,4072
Non-polymers8214
Water7,530418
1
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1764
Polymers13,7041
Non-polymers4723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0522
Polymers13,7041
Non-polymers3481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.208, 57.784, 70.446
Angle α, β, γ (deg.)90.00, 108.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1020-

HOH

21A-1079-

HOH

31A-1125-

HOH

41A-1142-

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.: 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-B0H / ~{N}-[4-[[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]methyl]-1,3-thiazol-2-yl]-2,4-dimethyl-1,3-oxazole-5-carboxamide


Mass: 348.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24N4O2S
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris Propane pH9, 10% EG, 0.15M NaNO3, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999989 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 1.65→43.89 Å / Num. obs: 32602 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 18
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1588 / CC1/2: 0.879 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Mantiddata reduction
ADDREFdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 1.65→43.886 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.63
RfactorNum. reflection% reflection
Rfree0.1816 2000 6.14 %
Rwork0.1569 --
obs0.1584 32597 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→43.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 56 418 2329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091966
X-RAY DIFFRACTIONf_angle_d1.0332655
X-RAY DIFFRACTIONf_dihedral_angle_d7.8361688
X-RAY DIFFRACTIONf_chiral_restr0.044284
X-RAY DIFFRACTIONf_plane_restr0.005347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69130.22661430.18822186X-RAY DIFFRACTION100
1.6913-1.7370.2371400.18422143X-RAY DIFFRACTION100
1.737-1.78810.22471430.18612187X-RAY DIFFRACTION100
1.7881-1.84590.23761420.1812178X-RAY DIFFRACTION100
1.8459-1.91180.24451440.17562199X-RAY DIFFRACTION100
1.9118-1.98840.19811430.17472186X-RAY DIFFRACTION100
1.9884-2.07890.20291420.16322171X-RAY DIFFRACTION100
2.0789-2.18850.18241420.15452180X-RAY DIFFRACTION100
2.1885-2.32560.18711420.15862180X-RAY DIFFRACTION100
2.3256-2.50510.20131440.15972191X-RAY DIFFRACTION100
2.5051-2.75720.17431430.16122195X-RAY DIFFRACTION100
2.7572-3.15610.16341430.15412185X-RAY DIFFRACTION100
3.1561-3.97590.15071440.13412199X-RAY DIFFRACTION99
3.9759-43.9020.15951450.14912217X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 30.6951 Å / Origin y: 8.3596 Å / Origin z: 19.2005 Å
111213212223313233
T0.1021 Å20.0017 Å2-0.0226 Å2-0.0974 Å20.0073 Å2--0.0921 Å2
L0.1745 °20.1959 °2-0.2491 °2-0.2614 °20.0783 °2--0.4052 °2
S0.0608 Å °-0.0764 Å °-0.0734 Å °0.0955 Å °-0.0155 Å °-0.0569 Å °-0.0438 Å °0.0715 Å °-0.0051 Å °
Refinement TLS groupSelection details: all

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