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- PDB-6lu6: Crystal structure of BPTF-BRD with ligand DCBPin5-2 bound -

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Basic information

Entry
Database: PDB / ID: 6lu6
TitleCrystal structure of BPTF-BRD with ligand DCBPin5-2 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-EUU / Bromodomain PHD finger transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97006302049 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 26, 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)13,4472
Polymers13,0321
Non-polymers4161
Water46826
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6740 Å2
Unit cell
Length a, b, c (Å)111.424, 27.141, 38.758
Angle α, β, γ (deg.)90.000, 98.130, 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: 13031.885 Da / Num. of mol.: 1 / Fragment: Bromodomain
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-EUU / 6-[1-[3-(dimethylamino)propyl]indol-5-yl]-2-methylsulfonyl-N-propyl-pyrimidin-4-amine


Mass: 415.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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 %
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% PEG3350

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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 PILATUS 6M / Detector: PIXEL / Date: Dec 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.97→33.82 Å / Num. obs: 7299 / % possible obs: 88.7 % / Redundancy: 2.2 % / Biso Wilson estimate: 25.5461904813 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1108 / Rpim(I) all: 0.1108 / Rrim(I) all: 0.1567 / Net I/σ(I): 2.2
Reflection shellResolution: 1.97→2.04 Å / Rmerge(I) obs: 0.9473 / Num. unique obs: 753 / CC1/2: 0.841 / Rpim(I) all: 0.9473

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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: 1.97006302049→33.8181389703 Å / SU ML: 0.450709209554 / Cross valid method: FREE R-VALUE / σ(F): 1.34349388682 / Phase error: 44.6521649335
RfactorNum. reflection% reflection
Rfree0.31607903768 382 5.27770102238 %
Rwork0.25335168471 --
obs0.257002223821 7238 86.4858406022 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.121167247 Å2
Refinement stepCycle: LAST / Resolution: 1.97006302049→33.8181389703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 29 26 970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774276877078982
X-RAY DIFFRACTIONf_angle_d0.911600626091339
X-RAY DIFFRACTIONf_chiral_restr0.0513320100938136
X-RAY DIFFRACTIONf_plane_restr0.00687742846647172
X-RAY DIFFRACTIONf_dihedral_angle_d23.2390107298594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.040.452121450361270.3624169384192310X-RAY DIFFRACTION88.7472687546
2.04-2.84090.3433648992851190.2924451347682305X-RAY DIFFRACTION87.8260869565
2.8409-33.810.273048912811360.2027738298662241X-RAY DIFFRACTION83.0828381685

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