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- PDB-6lu5: Crystal structure of BPTF-BRD with ligand DCBPin5 bound -

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Basic information

Entry
Database: PDB / ID: 6lu5
TitleCrystal structure of BPTF-BRD with ligand DCBPin5 bound
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsANTITUMOR PROTEIN / BPTF Bromodomain / Lysine acetylation / small-molecule inhibitor / high-throughput screening / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


NURF complex / regulation of transcription by RNA polymerase II / zinc ion binding
Similarity search - Function
Nucleosome-remodeling factor subunit BPTF / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Nucleosome-remodeling factor subunit BPTF / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / 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
Similarity search - Domain/homology
Chem-EUO / Bromodomain PHD finger transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86527732574 Å
AuthorsLu, T. / Lu, H.B. / Wang, J. / Lin, H. / Lu, W. / Luo, C.
CitationJournal: To Be Published
Title: Discovery and Optimization of Small-Molecule Inhibitors for the BPTF Bromodomains Proteins
Authors: Lu, T. / Lu, H.B. / Wang, J. / Han, J. / Xiao, S. / Jiang, H. / Chen, Y. / Yang, F. / Li, Q. / Jiang, H.L. / Chen, K.X. / Lu, W.C. / Lin, H. / Luo, C.
History
DepositionJan 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Nucleosome-remodeling factor subunit BPTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1642
Polymers12,8621
Non-polymers3021
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6510 Å2
Unit cell
Length a, b, c (Å)110.173, 26.987, 37.552
Angle α, β, γ (deg.)90.000, 95.828, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Nucleosome-remodeling factor subunit BPTF


Mass: 12861.676 Da / Num. of mol.: 1 / Fragment: Bromodomain PHD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF / Production host: Escherichia coli (E. coli) / References: UniProt: J3QQQ8
#2: Chemical ChemComp-EUO / 6-(1H-indol-5-yl)-N-methyl-2-methylsulfonyl-pyrimidin-4-amine


Mass: 302.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.865→32.44 Å / Num. obs: 9222 / % possible obs: 94.86 % / Redundancy: 6.2 % / Biso Wilson estimate: 13.1143879973 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.03 / Rrim(I) all: 0.076 / Rsym value: 0.069 / Net I/σ(I): 9.7
Reflection shellResolution: 1.865→1.932 Å / Rmerge(I) obs: 0.235 / Num. unique obs: 715 / CC1/2: 0.969 / CC star: 0.992 / Rpim(I) all: 0.109 / Rrim(I) all: 0.26 / Rsym value: 0.235

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QZT

3qzt


Resolution: 1.86527732574→32.4390256796 Å / SU ML: 0.244369917274 / Cross valid method: NONE / σ(F): 1.37572142191 / Phase error: 28.0082464013
RfactorNum. reflection% reflection
Rfree0.282140162555 423 4.72572896883 %
Rwork0.205750839555 --
obs0.209330457279 8951 94.8902788084 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.0386335406 Å2
Refinement stepCycle: LAST / Resolution: 1.86527732574→32.4390256796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 21 86 1011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007946015350591001
X-RAY DIFFRACTIONf_angle_d0.9552955804151368
X-RAY DIFFRACTIONf_chiral_restr0.0468525499047139
X-RAY DIFFRACTIONf_plane_restr0.00563171670177176
X-RAY DIFFRACTIONf_dihedral_angle_d18.4133961811619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.865-1.9320.2944410272071130.2031410348872593X-RAY DIFFRACTION87.657920311
1.932-2.68990.3054865062641550.2071915781552968X-RAY DIFFRACTION99.1743410607
2.6899-3.3590.2640131053021550.2058171072841589X-RAY DIFFRACTION98.82

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