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- PDB-5wmg: N-terminal bromodomain of BRD4 in complex with OTX-015 -

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Basic information

Entry
Database: PDB / ID: 5wmg
TitleN-terminal bromodomain of BRD4 in complex with OTX-015
ComponentsBromodomain-containing protein 4BRD4
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / bromodomain / BRD4 / transcription / PLX51107 / transcription-transcription inhibitor complex
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-like / Histone Acetyltransferase; Chain A ...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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6JF / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsZhang, Y.
CitationJournal: Cancer Discov / Year: 2018
Title: BRD4 Profiling Identifies Critical Chronic Lymphocytic Leukemia Oncogenic Circuits and Reveals Sensitivity to PLX51107, a Novel Structurally Distinct BET Inhibitor.
Authors: Ozer, H.G. / El-Gamal, D. / Powell, B. / Hing, Z.A. / Blachly, J.S. / Harrington, B. / Mitchell, S. / Grieselhuber, N.R. / Williams, K. / Lai, T.H. / Alinari, L. / Baiocchi, R.A. / Brinton, ...Authors: Ozer, H.G. / El-Gamal, D. / Powell, B. / Hing, Z.A. / Blachly, J.S. / Harrington, B. / Mitchell, S. / Grieselhuber, N.R. / Williams, K. / Lai, T.H. / Alinari, L. / Baiocchi, R.A. / Brinton, L. / Baskin, E. / Cannon, M. / Beaver, L. / Goettl, V.M. / Lucas, D.M. / Woyach, J.A. / Sampath, D. / Lehman, A.M. / Yu, L. / Zhang, J. / Ma, Y. / Zhang, Y. / Spevak, W. / Shi, S. / Severson, P. / Shellooe, R. / Carias, H. / Tsang, G. / Dong, K. / Ewing, T. / Marimuthu, A. / Tantoy, C. / Walters, J. / Sanftner, L. / Rezaei, H. / Nespi, M. / Matusow, B. / Habets, G. / Ibrahim, P. / Zhang, C. / Mathe, E.A. / Bollag, G. / Byrd, J.C. / Lapalombella, R.
History
DepositionJul 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6505
Polymers15,0251
Non-polymers6254
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint8 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.825, 42.217, 92.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15025.343 Da / Num. of mol.: 1 / Fragment: N-terminal bromodomain (UNP residues 44-168) / Mutation: D96A
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-6JF / 4-{6-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1S)-1-(pyridin-2-yl)ethyl]-1H-pyrrolo[3,2-b]pyridin-3-yl}benzoic acid


Mass: 438.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H22N4O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Bis-Tris, pH 7.5, 19% PEG3350, 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 51717 / % possible obs: 94.3 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 20.8
Reflection shellResolution: 1.15→1.19 Å / Rmerge(I) obs: 0.486

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WMA

5wma


Resolution: 1.19→24.14 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.74
RfactorNum. reflection% reflection
Rfree0.146 2441 5.08 %
Rwork0.13 --
obs0.13 48029 96.9 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 52.58 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1751 Å20 Å20 Å2
2---1.7636 Å20 Å2
3---1.5885 Å2
Refinement stepCycle: LAST / Resolution: 1.19→24.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 45 265 1367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041164
X-RAY DIFFRACTIONf_angle_d1.0171590
X-RAY DIFFRACTIONf_dihedral_angle_d11.758462
X-RAY DIFFRACTIONf_chiral_restr0.057165
X-RAY DIFFRACTIONf_plane_restr0.005203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.21430.26721290.27052460X-RAY DIFFRACTION90
1.2143-1.24070.22931540.23882577X-RAY DIFFRACTION95
1.2407-1.26960.21151450.19542596X-RAY DIFFRACTION96
1.2696-1.30130.19221440.1622636X-RAY DIFFRACTION96
1.3013-1.33650.15841420.13552639X-RAY DIFFRACTION97
1.3365-1.37580.13981580.11452630X-RAY DIFFRACTION97
1.3758-1.42020.13811350.10492631X-RAY DIFFRACTION97
1.4202-1.4710.13641600.09492689X-RAY DIFFRACTION97
1.471-1.52990.11461600.08782633X-RAY DIFFRACTION98
1.5299-1.59950.12351600.08542718X-RAY DIFFRACTION98
1.5995-1.68380.13441330.0922712X-RAY DIFFRACTION98
1.6838-1.78930.12721460.09482722X-RAY DIFFRACTION99
1.7893-1.92740.11591380.10042756X-RAY DIFFRACTION99
1.9274-2.12120.14341350.10772786X-RAY DIFFRACTION100
2.1212-2.42790.12181300.11582811X-RAY DIFFRACTION100
2.4279-3.05790.14611400.1332841X-RAY DIFFRACTION100
3.0579-24.14070.16711320.16672751X-RAY DIFFRACTION92

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