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- PDB-9nn5: BET BRD4-BD1 in complex with peptide 9.2 -

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Basic information

Entry
Database: PDB / ID: 9nn5
TitleBET BRD4-BD1 in complex with peptide 9.2
Components
  • Bromodomain-containing protein 4
  • peptide 9.2
KeywordsTRANSCRIPTION / Transcription regulator/inhibitor
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: 1.47 Å
AuthorsJing, X. / Mackay, J.P.
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 5, 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: peptide 9.2


Theoretical massNumber of molelcules
Total (without water)16,8432
Polymers16,8432
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-13 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.722, 42.067, 29.703
Angle α, β, γ (deg.)90.000, 92.190, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 15342.529 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 BL21(DE3) (bacteria) / References: UniProt: O60885
#2: Protein/peptide peptide 9.2


Mass: 1500.849 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium chloride, 20% w/v Polyethylene glycol 3,350

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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: Jun 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.47→39.82 Å / Num. obs: 25963 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.62 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.3
Reflection shellResolution: 1.47→1.5 Å / Rmerge(I) obs: 0.615 / Num. unique obs: 25961

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→39.82 Å / SU ML: 0.1309 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.82
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1927 2003 7.71 %
Rwork0.1678 23960 -
obs0.1698 25963 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.54 Å2
Refinement stepCycle: LAST / Resolution: 1.47→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1154 0 4 148 1306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891190
X-RAY DIFFRACTIONf_angle_d1.09271616
X-RAY DIFFRACTIONf_chiral_restr0.0783171
X-RAY DIFFRACTIONf_plane_restr0.009207
X-RAY DIFFRACTIONf_dihedral_angle_d5.6058157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.510.23951500.2241668X-RAY DIFFRACTION99.45
1.51-1.550.20521340.19351727X-RAY DIFFRACTION99.36
1.55-1.590.20451400.1891682X-RAY DIFFRACTION99.89
1.59-1.650.19991480.17941717X-RAY DIFFRACTION99.84
1.65-1.70.22991360.18471676X-RAY DIFFRACTION99.56
1.7-1.770.2151440.18181739X-RAY DIFFRACTION99.79
1.77-1.850.19881480.17281688X-RAY DIFFRACTION99.78
1.85-1.950.18821370.17151680X-RAY DIFFRACTION98.75
1.95-2.070.19751440.16821715X-RAY DIFFRACTION99.73
2.07-2.230.16181450.15231716X-RAY DIFFRACTION99.73
2.23-2.460.20451390.1621735X-RAY DIFFRACTION99.68
2.46-2.810.19641390.16151721X-RAY DIFFRACTION99.79
2.81-3.540.1991500.16421706X-RAY DIFFRACTION99.3
3.55-39.820.17751490.16481790X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: -17.681 Å / Origin y: 23.969 Å / Origin z: 11.714 Å
111213212223313233
T0.15493625063 Å2-0.0334602988883 Å20.0385296236752 Å2-0.155283724616 Å2-0.0402908310333 Å2--0.184279509993 Å2
L2.67831537568 °20.925056996857 °2-1.13954811033 °2-1.6602516505 °2-0.638837768957 °2--1.97322876129 °2
S0.122584923518 Å °-0.137452848189 Å °-0.0227748790889 Å °0.236461195724 Å °-0.169744334013 Å °0.171630255218 Å °0.00332298659784 Å °0.0880271919782 Å °0.0462498713683 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:167 OR RESID 201:335 ) ) OR ( CHAIN B AND ( RESID 15:26 OR RESID 101:113 ) )A42 - 167
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:167 OR RESID 201:335 ) ) OR ( CHAIN B AND ( RESID 15:26 OR RESID 101:113 ) )A201 - 335
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:167 OR RESID 201:335 ) ) OR ( CHAIN B AND ( RESID 15:26 OR RESID 101:113 ) )B15 - 26
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 42:167 OR RESID 201:335 ) ) OR ( CHAIN B AND ( RESID 15:26 OR RESID 101:113 ) )B101 - 113

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