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- PDB-6u61: BRD2-BD1 in complex with the cyclic peptide 3.1_3 -

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Basic information

Entry
Database: PDB / ID: 6u61
TitleBRD2-BD1 in complex with the cyclic peptide 3.1_3
Components
  • Bromodomain-containing protein 2
  • cyclic peptide 3.1_3
KeywordsTRANSCRIPTION/INHIBITOR / BET / bromodomain / macrocyclic peptide / BRD2 / inhibitor / RaPID / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / chromosome / chromatin organization / spermatogenesis / histone binding / protein-macromolecule adaptor activity / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of DNA-templated transcription / 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 / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsPatel, K. / Walshe, J.L. / Walport, L.J. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1161623 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Cyclic peptides can engage a single binding pocket through highly divergent modes.
Authors: Patel, K. / Walport, L.J. / Walshe, J.L. / Solomon, P.D. / Low, J.K.K. / Tran, D.H. / Mouradian, K.S. / Silva, A.P.G. / Wilkinson-White, L. / Norman, A. / Franck, C. / Matthews, J.M. / Guss, ...Authors: Patel, K. / Walport, L.J. / Walshe, J.L. / Solomon, P.D. / Low, J.K.K. / Tran, D.H. / Mouradian, K.S. / Silva, A.P.G. / Wilkinson-White, L. / Norman, A. / Franck, C. / Matthews, J.M. / Guss, J.M. / Payne, R.J. / Passioura, T. / Suga, H. / Mackay, J.P.
History
DepositionAug 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
E: cyclic peptide 3.1_3
D: cyclic peptide 3.1_3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9177
Polymers34,7214
Non-polymers1963
Water1,38777
1
A: Bromodomain-containing protein 2
E: cyclic peptide 3.1_3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4914
Polymers17,3602
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-61 kcal/mol
Surface area7550 Å2
MethodPISA
2
B: Bromodomain-containing protein 2
D: cyclic peptide 3.1_3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4263
Polymers17,3602
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-44 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.538, 86.752, 115.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Bromodomain-containing protein 2


Mass: 15893.472 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2 / Production host: Escherichia coli (E. coli) / References: UniProt: H0Y6K2, UniProt: P25440*PLUS
#2: Protein/peptide cyclic peptide 3.1_3


Mass: 1466.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.01 M Zinc chloride, 0.1 M MES pH 6.0, 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: Feb 23, 2018
RadiationMonochromator: 0.9537 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.29→49.11 Å / Num. obs: 16100 / % possible obs: 99.6 % / Redundancy: 12.7 % / Biso Wilson estimate: 38.79 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.9
Reflection shellResolution: 2.29→2.37 Å / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1500 / CC1/2: 0.874

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONI

3oni


Resolution: 2.29→43.38 Å / SU ML: 0.299 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.54
RfactorNum. reflection% reflection
Rfree0.263 826 5.14 %
Rwork0.222 --
obs0.224 16071 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.16 Å2
Refinement stepCycle: LAST / Resolution: 2.29→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 3 77 2253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022235
X-RAY DIFFRACTIONf_angle_d0.5193013
X-RAY DIFFRACTIONf_dihedral_angle_d10.5541347
X-RAY DIFFRACTIONf_chiral_restr0.039313
X-RAY DIFFRACTIONf_plane_restr0.003377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.430.34221500.29232423X-RAY DIFFRACTION98
2.43-2.620.33081250.2692532X-RAY DIFFRACTION100
2.62-2.880.27711330.2562526X-RAY DIFFRACTION100
2.88-3.30.26951430.23922542X-RAY DIFFRACTION100
3.3-4.160.24381350.20132551X-RAY DIFFRACTION100
4.16-43.380.24051400.1982671X-RAY DIFFRACTION100

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