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- PDB-6xuz: CRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 4 -

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Basic information

Entry
Database: PDB / ID: 6xuz
TitleCRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 4
ComponentsBromodomain-containing protein 4BRD4
KeywordsTRANSCRIPTION / BROMODOMAIN / 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-O1W / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsBader, G. / Kessler, D. / Wolkerstorfer, B.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: PI by NMR: Probing CH-pi Interactions in Protein-Ligand Complexes by NMR Spectroscopy.
Authors: Platzer, G. / Mayer, M. / Beier, A. / Bruschweiler, S. / Fuchs, J.E. / Engelhardt, H. / Geist, L. / Bader, G. / Schorghuber, J. / Lichtenecker, R. / Wolkerstorfer, B. / Kessler, D. / McConnell, D.B. / Konrat, R.
History
DepositionJan 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.title / _citation_author.name / _software.name
Revision 1.2Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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)15,5792
Polymers15,0991
Non-polymers4801
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.857, 48.287, 57.885
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15099.380 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-O1W / 6-[1-[(2~{S})-1-methoxypropan-2-yl]-6-[(3~{S})-3-methylmorpholin-4-yl]imidazo[4,5-c]pyridin-2-yl]-3-methyl-~{N}-propan-2-yl-[1,2,4]triazolo[4,3-a]pyrazin-8-amine


Mass: 479.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H33N9O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.94 Å3/Da / Density % sol: 36.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 29% PEG 3350, 0.2 M disodium malonate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.07→37.0795 Å / Num. obs: 40107 / % possible obs: 76.4 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 10.7
Reflection shellResolution: 1.07→1.144 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.449 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2441 / Rsym value: 1.449 / % possible all: 21.4

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
autoPROCdata reduction
XDSJan 26, 201data reduction
autoPROC1.1.7data scaling
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OSS

2oss


Resolution: 1.07→37.08 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.044 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.045 / SU Rfree Blow DPI: 0.047 / SU Rfree Cruickshank DPI: 0.043
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 1942 -RANDOM
Rwork0.1772 ---
obs0.1784 40102 76.5 %-
Displacement parametersBiso mean: 16.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.2336 Å20 Å20 Å2
2--0.1137 Å20 Å2
3---0.1199 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.07→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 35 220 1317
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012292HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.954167HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d657SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes330HARMONIC5
X-RAY DIFFRACTIONt_it1092HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion144SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2272SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.96
X-RAY DIFFRACTIONt_other_torsion12.8
LS refinement shellResolution: 1.07→1.12 Å
RfactorNum. reflection% reflection
Rfree0.2341 47 -
Rwork0.1923 --
obs0.1945 803 13.22 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.10410.03060.02610.1616-0.07130.143-0.00010.0003-0.00040.00030.00020.0004-0.00040.0004-0.00010.0048-0.00130.00070.00580.00240.003813.86398.308811.8055
20.0016-0.00130.00070.00030.00010.00070-00-00000-00.00040.0001-00.00050.00020.00063.73867.210723.1074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|42 to 168 }A42 - 168
2X-RAY DIFFRACTION2{ A|201}A201

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