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- PDB-6xv3: CRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 3 -

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Basic information

Entry
Database: PDB / ID: 6xv3
TitleCRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 3
ComponentsBromodomain-containing protein 4
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 / chromatin / 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-O2B / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 23, 2021Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: Bromodomain-containing protein 4
C: Bromodomain-containing protein 4
D: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4448
Polymers60,3984
Non-polymers2,0464
Water12,034668
1
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6112
Polymers15,0991
Non-polymers5121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6112
Polymers15,0991
Non-polymers5121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6112
Polymers15,0991
Non-polymers5121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6112
Polymers15,0991
Non-polymers5121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.184, 58.955, 59.639
Angle α, β, γ (deg.)105.250, 90.700, 97.940
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 15099.380 Da / Num. of mol.: 4
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-O2B / 3-methyl-6-[6-[(3~{S})-3-methylmorpholin-4-yl]-1-[(1~{S})-1-phenylethyl]imidazo[4,5-c]pyridin-2-yl]-~{N}-propan-2-yl-[1,2,4]triazolo[4,3-a]pyrazin-8-amine


Mass: 511.621 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H33N9O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
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 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→56.26 Å / Num. obs: 57389 / % possible obs: 82.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 16.32 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.3
Reflection shellResolution: 1.47→1.59 Å / Num. unique obs: 2892 / CC1/2: 0.579

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OSS

2oss


Resolution: 1.47→36.15 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.89 / SU R Cruickshank DPI: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.154 / SU Rfree Cruickshank DPI: 0.149
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2863 4.99 %RANDOM
Rwork0.259 ---
obs0.261 57389 61.1 %-
Displacement parametersBiso max: 135.79 Å2 / Biso mean: 19.56 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.7311 Å2-0.2336 Å2-0.24 Å2
2--1.4928 Å20.905 Å2
3----0.7618 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 1.47→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 152 668 5068
Biso mean--14.58 27.95 -
Num. residues----508
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1929SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1493HARMONIC5
X-RAY DIFFRACTIONt_it8945HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion577SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9144SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8945HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg16264HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion14.99
LS refinement shellResolution: 1.47→1.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.239 57 4.97 %
Rwork0.2478 1091 -
all0.2474 1148 -
obs--8.13 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-12.8906-23.626241.8688
2-10.6981-16.377513.5888
39.3237-39.5692.1513
49.6422-47.022630.528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A42 - 168
2X-RAY DIFFRACTION2{ B|* }B42 - 168
3X-RAY DIFFRACTION3{ C|* }C42 - 168
4X-RAY DIFFRACTION4{ D|* }D42 - 168

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