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- PDB-5y8c: Crystal Structure Analysis of the BRD4 -

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Basic information

Entry
Database: PDB / ID: 5y8c
TitleCrystal Structure Analysis of the BRD4
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / BRD4(1) / Bromodomain
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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-8P9 / NITRATE ION / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsXu, Y. / Zhang, Y. / Song, M. / Wang, C.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structure-Based Discovery and Optimization of Benzo[ d]isoxazole Derivatives as Potent and Selective BET Inhibitors for Potential Treatment of Castration-Resistant Prostate Cancer (CRPC)
Authors: Zhang, M. / Zhang, Y. / Song, M. / Xue, X. / Wang, J. / Wang, C. / Zhang, C. / Li, C. / Xiang, Q. / Zou, L. / Wu, X. / Wu, C. / Dong, B. / Xue, W. / Zhou, Y. / Chen, H. / Wu, D. / Ding, K. / Xu, Y.
History
DepositionAug 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2327
Polymers16,5091
Non-polymers7236
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint1 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.200, 47.200, 78.069
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 16509.100 Da / Num. of mol.: 1 / Fragment: UNP residues 44-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O60885

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Non-polymers , 5 types, 66 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-8P9 / 5-chloranyl-2-methoxy-N-(6-methoxy-3-methyl-1,2-benzoxazol-5-yl)benzenesulfonamide


Mass: 382.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15ClN2O5S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.98 Å3/Da / Density % sol: 37.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH 8.2

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.42→78.07 Å / Num. obs: 25180 / % possible obs: 99.8 % / Redundancy: 11.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.025 / Rrim(I) all: 0.087 / Net I/σ(I): 16.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.42-1.4511.80.4512330.9830.1350.4799.9
7.78-78.0710.30.0942010.9940.0280.09999.8

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXF

3mxf


Resolution: 1.42→40.39 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.079 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.071
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 1248 5 %RANDOM
Rwork0.188 ---
obs0.1892 23875 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 48.67 Å2 / Biso mean: 17.903 Å2 / Biso min: 9.99 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å20 Å2-0 Å2
2---1.14 Å20 Å2
3----0.97 Å2
Refinement stepCycle: final / Resolution: 1.42→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1122 0 47 60 1229
Biso mean--22.34 22.91 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021220
X-RAY DIFFRACTIONr_bond_other_d0.0030.021149
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9831658
X-RAY DIFFRACTIONr_angle_other_deg0.9283.0042649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2745137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9225.08559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49715205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211357
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02285
LS refinement shellResolution: 1.421→1.458 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 99 -
Rwork0.214 1745 -
all-1844 -
obs--99.84 %

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