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- PDB-7eig: BRD4-BD1 in complex with LT-730-903 -

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Basic information

Entry
Database: PDB / ID: 7eig
TitleBRD4-BD1 in complex with LT-730-903
ComponentsBromodomain-containing protein 4BRD4
KeywordsGENE REGULATION / Inhibitor / BRD4 / BD1
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-N03 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsZheng, W. / Kong, B. / Tang, W. / Zhu, J. / Chen, Y.
CitationJournal: To Be Published
Title: BRD4-BD1 in complex with LT-730-903
Authors: Zheng, W. / Kong, B. / Tang, W. / Zhu, J. / Chen, Y.
History
DepositionMar 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2142
Polymers14,8831
Non-polymers3301
Water3,009167
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 area7470 Å2
Unit cell
Length a, b, c (Å)31.230, 46.980, 79.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing protein 4 / BRD4 / Protein HUNK1


Mass: 14883.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-N03 / 1-[5-(5-azanyl-1H-benzimidazol-2-yl)-2-methyl-4-phenyl-1H-pyrrol-3-yl]ethanone


Mass: 330.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.95 Å3/Da / Density % sol: 36.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 4 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.3→40.381 Å / Num. obs: 26945 / % possible obs: 92.3 % / Redundancy: 9.3 % / CC1/2: 0.972 / Rmerge(I) obs: 0.168 / Net I/σ(I): 8.2
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.381 / Num. unique obs: 1116 / CC1/2: 0.927

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3235refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UY9

5uy9


Resolution: 1.3→40.381 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2016 1288 4.79 %
Rwork0.1811 25612 -
obs0.182 26900 91.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.02 Å2 / Biso mean: 17.6134 Å2 / Biso min: 5.02 Å2
Refinement stepCycle: final / Resolution: 1.3→40.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 25 167 1238
Biso mean--32.38 28.5 -
Num. residues----125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.35210.24261440.2179252583
1.3521-1.41360.26831240.2093270688
1.4136-1.48820.21891430.1916272489
1.4882-1.58140.18371120.1859274489
1.5814-1.70350.21741490.1787284993
1.7035-1.87490.21031520.1846293395
1.8749-2.14620.19891690.1659287593
2.1462-2.70390.17741550.1779305397
2.7039-40.3810.19821400.1793320397
Refinement TLS params.Method: refined / Origin x: 22.149 Å / Origin y: 20.1127 Å / Origin z: 48.0954 Å
111213212223313233
T0.0769 Å2-0.0011 Å20.0135 Å2-0.0772 Å2-0.0099 Å2--0.0779 Å2
L0.5342 °20.1655 °2-0.0751 °2-0.7423 °2-0.2213 °2--0.8917 °2
S-0.0104 Å °0.0026 Å °-0.0019 Å °-0.0588 Å °0.0127 Å °-0.0595 Å °0.0317 Å °0.0046 Å °0.0016 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 125
2X-RAY DIFFRACTION1allA201
3X-RAY DIFFRACTION1allS1 - 167

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