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- PDB-7zfz: BRD4 in complex with PepLite-Val -

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Basic information

Entry
Database: PDB / ID: 7zfz
TitleBRD4 in complex with PepLite-Val
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / FragLites / anomalous / BRD4 / Fragment screening
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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader 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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader 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 I / Brdt, bromodomain, repeat II / 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 I / Brdt, bromodomain, repeat II / 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-IT8 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsTurberville, S. / Martin, M.P. / Hope, I. / Noble, M.E.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKC57659/A27310 United Kingdom
Cancer Research UKC1362/A20263 United Kingdom
Cancer Research UKC2215/A21421 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Mapping Ligand Interactions of Bromodomains BRD4 and ATAD2 with FragLites and PepLites─Halogenated Probes of Druglike and Peptide-like Molecular Interactions.
Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / ...Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / Endicott, J.A. / Hardcastle, I.R. / Noble, M.E.M. / Waring, M.J.
History
DepositionApr 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7544
Polymers15,2951
Non-polymers4593
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-1 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.808, 43.417, 79.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15294.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IT8 / (2R)-2-acetamido-N-(3-bromanylprop-2-ynyl)-3-methyl-butanamide


Mass: 275.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15BrN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.95397 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95397 Å / Relative weight: 1
ReflectionResolution: 1.08→39.68 Å / Num. obs: 54177 / % possible obs: 95.5 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.045 / Rrim(I) all: 0.086 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
5.92-39.685.60.054280.9940.0320.059
1.08-1.13.11.41317160.3271.1361.821

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LRQ

5lrq


Resolution: 1.08→39.68 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.771 / SU ML: 0.035 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2364 2655 4.907 %
Rwork0.2056 51456 -
all0.207 --
obs-54111 95.182 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.505 Å2
Baniso -1Baniso -2Baniso -3
1-0.381 Å20 Å2-0 Å2
2---0.298 Å20 Å2
3----0.083 Å2
Refinement stepCycle: LAST / Resolution: 1.08→39.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 27 145 1248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121154
X-RAY DIFFRACTIONr_angle_refined_deg2.0781.6551570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32624.560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5515203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.845153
X-RAY DIFFRACTIONr_chiral_restr0.1150.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02887
X-RAY DIFFRACTIONr_nbd_refined0.2450.2569
X-RAY DIFFRACTIONr_nbtor_refined0.3240.2787
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.292
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.229
X-RAY DIFFRACTIONr_mcbond_it1.3351.304527
X-RAY DIFFRACTIONr_mcangle_it1.9881.956661
X-RAY DIFFRACTIONr_scbond_it3.6431.685627
X-RAY DIFFRACTIONr_scangle_it4.8262.391908
X-RAY DIFFRACTIONr_lrange_it6.93520.5251841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.1080.371310.3442520X-RAY DIFFRACTION63.9874
1.108-1.1380.3491590.3283045X-RAY DIFFRACTION79.3659
1.138-1.1710.3121830.3093512X-RAY DIFFRACTION93.7817
1.171-1.2070.2922020.2843569X-RAY DIFFRACTION98.4595
1.207-1.2470.2781550.2713521X-RAY DIFFRACTION99.5397
1.247-1.2910.2521840.2513370X-RAY DIFFRACTION99.1906
1.291-1.340.2461420.2283334X-RAY DIFFRACTION99.8851
1.34-1.3940.2241740.2153167X-RAY DIFFRACTION99.4641
1.394-1.4560.2231680.2043040X-RAY DIFFRACTION99.5346
1.456-1.5270.2081570.1922909X-RAY DIFFRACTION100
1.527-1.610.2231260.1832802X-RAY DIFFRACTION100
1.61-1.7070.2261510.1822633X-RAY DIFFRACTION99.8207
1.707-1.8250.211160.1822478X-RAY DIFFRACTION99.8845
1.825-1.9710.2411270.1942342X-RAY DIFFRACTION99.9595
1.971-2.1590.2471100.2032141X-RAY DIFFRACTION100
2.159-2.4140.2271050.1971967X-RAY DIFFRACTION100
2.414-2.7870.204860.1931733X-RAY DIFFRACTION99.9451
2.787-3.4120.206700.1911508X-RAY DIFFRACTION99.9367
3.412-4.8210.206710.161168X-RAY DIFFRACTION100
4.821-39.680.331380.261697X-RAY DIFFRACTION100

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