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- PDB-9mpj: BRD2-BD1 in complex with cyclic peptide 2.1C -

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Basic information

Entry
Database: PDB / ID: 9mpj
TitleBRD2-BD1 in complex with cyclic peptide 2.1C
Components
  • 2.1C
  • Bromodomain-containing protein 2
KeywordsGENE REGULATION / BRD2 / cyclic peptide
Function / homology
Function and homology information


acetylation-dependent protein binding / histone H3K14ac reader activity / chromatin looping / histone H4K5ac reader activity / RUNX3 regulates p14-ARF / histone H4K12ac reader activity / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...acetylation-dependent protein binding / histone H3K14ac reader activity / chromatin looping / histone H4K5ac reader activity / RUNX3 regulates p14-ARF / histone H4K12ac reader activity / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / histone binding / spermatogenesis / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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 ...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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsPatel, K. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: BRD2-BD1 in complex with cyclic peptide 2.1C
Authors: Patel, K. / Mackay, J.P.
History
DepositionDec 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
D: Bromodomain-containing protein 2
E: 2.1C
F: 2.1C
G: 2.1C
H: 2.1C


Theoretical massNumber of molelcules
Total (without water)70,5068
Polymers70,5068
Non-polymers00
Water00
1
A: Bromodomain-containing protein 2
G: 2.1C


Theoretical massNumber of molelcules
Total (without water)17,6262
Polymers17,6262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-11 kcal/mol
Surface area7970 Å2
MethodPISA
2
B: Bromodomain-containing protein 2
E: 2.1C


Theoretical massNumber of molelcules
Total (without water)17,6262
Polymers17,6262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-11 kcal/mol
Surface area7940 Å2
MethodPISA
3
C: Bromodomain-containing protein 2
F: 2.1C


Theoretical massNumber of molelcules
Total (without water)17,6262
Polymers17,6262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-10 kcal/mol
Surface area7910 Å2
MethodPISA
4
D: Bromodomain-containing protein 2
H: 2.1C


Theoretical massNumber of molelcules
Total (without water)17,6262
Polymers17,6262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-10 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.625, 103.957, 105.074
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Bromodomain-containing protein 2 / O27.1.1


Mass: 15893.472 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Protein/peptide
2.1C


Mass: 1732.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.002 M Zinc chloride, 0.1 M Tris pH 8.0, 20 % w/v PEG 6000

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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: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.92→46.89 Å / Num. obs: 19351 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 46.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.176 / Net I/σ(I): 13.4
Reflection shellResolution: 2.92→3.09 Å / Rmerge(I) obs: 0.708 / Num. unique obs: 3047 / CC1/2: 0.897

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→46.89 Å / SU ML: 0.284 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0107
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2431 1021 5.29 %
Rwork0.2134 18278 -
obs0.215 19299 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.36 Å2
Refinement stepCycle: LAST / Resolution: 2.92→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 16 0 4612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184744
X-RAY DIFFRACTIONf_angle_d0.47056428
X-RAY DIFFRACTIONf_chiral_restr0.0382669
X-RAY DIFFRACTIONf_plane_restr0.0043811
X-RAY DIFFRACTIONf_dihedral_angle_d13.88731778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-3.070.29551290.2442544X-RAY DIFFRACTION99.26
3.07-3.260.31721310.24062586X-RAY DIFFRACTION100
3.26-3.520.28611650.23552561X-RAY DIFFRACTION100
3.52-3.870.2571510.20882585X-RAY DIFFRACTION100
3.87-4.430.22731520.20232595X-RAY DIFFRACTION100
4.43-5.580.21821250.20172665X-RAY DIFFRACTION100
5.58-46.890.20191680.20312742X-RAY DIFFRACTION99.83

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