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- PDB-7ush: BRD2-BD2 in complex with SF2523 -

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Basic information

Entry
Database: PDB / ID: 7ush
TitleBRD2-BD2 in complex with SF2523
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION/INHIBITOR / Inhibitor / acetyllysine binding pocket / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-82V / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsJayasinghe, T.D. / Ronning, D.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Control Release / Year: 2023
Title: Targeting BRD4 and PI3K signaling pathways for the treatment of medulloblastoma.
Authors: Sethi, B. / Kumar, V. / Jayasinghe, T.D. / Dong, Y. / Ronning, D.R. / Zhong, H.A. / Coulter, D.W. / Mahato, R.I.
History
DepositionApr 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7387
Polymers13,0561
Non-polymers6826
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.345, 71.732, 32.096
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

21A-731-

HOH

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Components

#1: Protein Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13056.032 Da / Num. of mol.: 1 / Fragment: BD2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical ChemComp-82V / 3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(morpholin-4-yl)-7H-thieno[3,2-b]pyran-7-one


Mass: 371.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17NO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 16 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 19, 2022
RadiationMonochromator: 0.98 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.27→29.59 Å / Num. obs: 32349 / % possible obs: 98.76 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.041 / Net I/σ(I): 28.8
Reflection shellResolution: 1.27→1.315 Å / Num. unique obs: 2972 / CC1/2: 0.699

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E6J

6e6j


Resolution: 1.27→29.59 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1913 1998 6.18 %
Rwork0.1669 30351 -
obs0.1684 32349 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.5 Å2 / Biso mean: 19.7579 Å2 / Biso min: 6.56 Å2
Refinement stepCycle: final / Resolution: 1.27→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 46 196 1157
Biso mean--27.7 29.78 -
Num. residues----111
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.27-1.30.25151290.28381957208691
1.3-1.340.27431390.25042112225196
1.34-1.370.27391380.22382096223499
1.37-1.420.21861420.209921522294100
1.42-1.470.20611430.186221732316100
1.47-1.530.20111430.182321962339100
1.53-1.60.20351430.166221732316100
1.6-1.680.19771430.164321562299100
1.68-1.790.17831460.16822142360100
1.79-1.930.19291440.170621922336100
1.93-2.120.18681440.165221862330100
2.12-2.430.20181430.16492172231599
2.43-3.060.17711460.1662226237299
3.06-29.590.17811550.14772346250199

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