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- PDB-9nnt: BET BRD4-BD1 in complex with peptide 6.1 -

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Basic information

Entry
Database: PDB / ID: 9nnt
TitleBET BRD4-BD1 in complex with peptide 6.1
Components
  • Bromodomain-containing protein 4
  • peptide 6.1
KeywordsTRANSCRIPTION / inhibitor / complex
Function / homology
Function and homology information


histone H4K8ac reader activity / histone H3K9ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription ...histone H4K8ac reader activity / histone H3K9ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription / histone H4K16ac reader activity / 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 / positive regulation of DNA-templated transcription / chromatin / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsJing, X.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Chem.Commun.(Camb.) / Year: 2026
Title: The effect of peptide size on target affinity in mRNA display-derived macrocyclic peptides.
Authors: Jing, X. / Suh, J. / Maxwell, J. / Patel, K. / Norman, A. / Reid, X.J. / Deshpande, C. / Low, J.K.K. / Payne, R.J. / Passioura, T. / Mackay, J.P.
History
DepositionMar 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Bromodomain-containing protein 4
C: Bromodomain-containing protein 4
D: peptide 6.1
E: peptide 6.1


Theoretical massNumber of molelcules
Total (without water)47,9095
Polymers47,9095
Non-polymers00
Water8,575476
1
A: Bromodomain-containing protein 4
D: peptide 6.1


Theoretical massNumber of molelcules
Total (without water)16,3482
Polymers16,3482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-12 kcal/mol
Surface area8300 Å2
MethodPISA
2
B: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)15,2131
Polymers15,2131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7810 Å2
MethodPISA
3
C: Bromodomain-containing protein 4
E: peptide 6.1


Theoretical massNumber of molelcules
Total (without water)16,3482
Polymers16,3482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-11 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.563, 41.628, 86.630
Angle α, β, γ (deg.)90.000, 92.600, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 15213.416 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885
#2: Protein/peptide peptide 6.1 / Protein HUNK1


Mass: 1134.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris 8.0 Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.59→48.33 Å / Num. obs: 53374 / % possible obs: 99.1 % / Redundancy: 7.1 % / Biso Wilson estimate: 18.78 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 8.6
Reflection shellResolution: 1.59→1.62 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 53372 / Rpim(I) all: 0.069

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→48.33 Å / SU ML: 0.1971 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.0066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2171 2012 3.77 %
Rwork0.1718 51361 -
obs0.1735 53373 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.1 Å2
Refinement stepCycle: LAST / Resolution: 1.59→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 22 476 3799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01153409
X-RAY DIFFRACTIONf_angle_d1.20184628
X-RAY DIFFRACTIONf_chiral_restr0.0548495
X-RAY DIFFRACTIONf_plane_restr0.0109596
X-RAY DIFFRACTIONf_dihedral_angle_d13.7314446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.30531190.30283000X-RAY DIFFRACTION81.1
1.63-1.680.31541340.24313668X-RAY DIFFRACTION98.4
1.68-1.730.27041470.223647X-RAY DIFFRACTION99.14
1.73-1.780.25981440.2053664X-RAY DIFFRACTION99.35
1.78-1.850.25751340.19323702X-RAY DIFFRACTION99.3
1.85-1.920.28321550.18963674X-RAY DIFFRACTION99.4
1.92-2.010.21191480.18213712X-RAY DIFFRACTION99.61
2.01-2.110.2211400.17543716X-RAY DIFFRACTION100
2.11-2.250.21241460.15683705X-RAY DIFFRACTION99.95
2.25-2.420.21021440.16753741X-RAY DIFFRACTION99.97
2.42-2.660.22591520.17313731X-RAY DIFFRACTION100
2.66-3.050.21151490.16573754X-RAY DIFFRACTION99.97
3.05-3.840.20931430.14853772X-RAY DIFFRACTION100
3.84-48.330.18181570.16173875X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -36.9970513446 Å / Origin y: 0.990772767543 Å / Origin z: -26.4706231423 Å
111213212223313233
T0.120657339393 Å2-0.00171997611234 Å20.00110074611887 Å2-0.103085734534 Å28.75270720834E-5 Å2--0.126609281295 Å2
L0.192899974047 °2-0.0313592516633 °20.0744336979954 °2--0.0258428840173 °2-0.0932328696621 °2--0.314729744865 °2
S-0.0193565865771 Å °-0.00499814748717 Å °-0.00185114705737 Å °-0.0110438797084 Å °0.0101149547913 Å °-0.00201754157007 Å °0.00313247189336 Å °-0.00126411282926 Å °-8.9094682591E-6 Å °
Refinement TLS groupSelection details: all

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