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- PDB-6lih: BRD4 BD1 bound with compound 10 -

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Basic information

Entry
Database: PDB / ID: 6lih
TitleBRD4 BD1 bound with compound 10
ComponentsBromodomain-containing protein 4
KeywordsGENE REGULATION / cancer / bromodomain
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 / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / 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-EDF / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6203054097 Å
AuthorsXiong, B. / Cao, D.
CitationJournal: To Be Published
Title: BRD4 BD1 bound with compound 10
Authors: Xiong, B. / Cao, D.
History
DepositionDec 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: 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)15,1422
Polymers14,7541
Non-polymers3871
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.071, 47.892, 77.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 14754.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O60885
#2: Chemical ChemComp-EDF / (3~{R})-1,3-dimethyl-6-[(4-phenylpyrimidin-2-yl)amino]-4-propan-2-yl-3~{H}-quinoxalin-2-one


Mass: 387.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7
Details: protein concentration 10 mg/ML, 2.8-3.8M sodium formate, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.62→40.81 Å / Num. obs: 29646 / % possible obs: 93.2 % / Redundancy: 9.5 % / Biso Wilson estimate: 17.1956118763 Å2 / CC1/2: 0.997 / Net I/σ(I): 16.3
Reflection shellResolution: 1.62→1.71 Å / Num. unique obs: 1559 / CC1/2: 0.841

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Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XHY

5xhy


Resolution: 1.6203054097→26.5985083072 Å / SU ML: 0.18060227712 / Cross valid method: FREE R-VALUE / σ(F): 1.3971772234 / Phase error: 25.2389332836
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.211721740316 2989 10.0823045267 %
Rwork0.188166833583 26657 -
obs0.190558037104 29646 91.9198809376 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.0563466282 Å2
Refinement stepCycle: LAST / Resolution: 1.6203054097→26.5985083072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 29 117 1183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006876216585321104
X-RAY DIFFRACTIONf_angle_d0.8407237327621507
X-RAY DIFFRACTIONf_chiral_restr0.0431072510155158
X-RAY DIFFRACTIONf_plane_restr0.00513539303701192
X-RAY DIFFRACTIONf_dihedral_angle_d13.8541460911668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62031-1.64690.466829122761730.445274272403700X-RAY DIFFRACTION49.5195387572
1.6469-1.67530.478009548113960.449573763064828X-RAY DIFFRACTION60.15625
1.6753-1.70570.4808598157081050.404790577043936X-RAY DIFFRACTION68.7582562748
1.7057-1.73850.3642529425761190.3209701782451062X-RAY DIFFRACTION76.9882659713
1.7385-1.7740.342991856881340.31074002981207X-RAY DIFFRACTION86.8523316062
1.774-1.81260.3405486397531510.2693003803711308X-RAY DIFFRACTION95.3594771242
1.8126-1.85470.3082672824611480.2090861884191348X-RAY DIFFRACTION96.082209377
1.8547-1.90110.2297631978641520.200629802631351X-RAY DIFFRACTION99.2734478203
1.9011-1.95250.2372369169161550.1777097968271385X-RAY DIFFRACTION99.7409326425
1.9525-2.00990.1854212332691480.1664517386071342X-RAY DIFFRACTION99.8659517426
2.0099-2.07480.2097609395081560.163214201521401X-RAY DIFFRACTION100
2.0748-2.14890.232244036971620.1609523023571374X-RAY DIFFRACTION99.8699609883
2.1489-2.23490.2085378131961530.1768699185931378X-RAY DIFFRACTION99.8695368558
2.2349-2.33650.2090225460571590.1722032965221392X-RAY DIFFRACTION99.9355670103
2.3365-2.45960.1950845441441530.1792402473671363X-RAY DIFFRACTION100
2.4596-2.61360.2117992764391580.1837554325561374X-RAY DIFFRACTION100
2.6136-2.81520.2309226437511510.1913684366321389X-RAY DIFFRACTION100
2.8152-3.09810.2107665331011520.188430411111380X-RAY DIFFRACTION100
3.0981-3.54550.177910009341590.1777039663211388X-RAY DIFFRACTION100
3.5455-4.46360.1359679414961550.1460775354291373X-RAY DIFFRACTION99.8040496408
4.4636-26.59850.1910029794661500.1828151311561378X-RAY DIFFRACTION99.6088657106

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