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- PDB-6swo: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH iBET-BD1 (GSK778) -

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Basic information

Entry
Database: PDB / ID: 6swo
TitleC-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH iBET-BD1 (GSK778)
ComponentsBromodomain-containing protein 2BRD2
KeywordsTRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD2 / BROMODOMAIN CONTAINING PROTEIN 2 / ANTAGONIST
Function / homology
Function and homology information


chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / 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-LWB / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.601 Å
AuthorsChung, C.
CitationJournal: Science / Year: 2020
Title: Selective targeting of BD1 and BD2 of the BET proteins in cancer and immunoinflammation.
Authors: Gilan, O. / Rioja, I. / Knezevic, K. / Bell, M.J. / Yeung, M.M. / Harker, N.R. / Lam, E.Y.N. / Chung, C.W. / Bamborough, P. / Petretich, M. / Urh, M. / Atkinson, S.J. / Bassil, A.K. / ...Authors: Gilan, O. / Rioja, I. / Knezevic, K. / Bell, M.J. / Yeung, M.M. / Harker, N.R. / Lam, E.Y.N. / Chung, C.W. / Bamborough, P. / Petretich, M. / Urh, M. / Atkinson, S.J. / Bassil, A.K. / Roberts, E.J. / Vassiliadis, D. / Burr, M.L. / Preston, A.G.S. / Wellaway, C. / Werner, T. / Gray, J.R. / Michon, A.M. / Gobbetti, T. / Kumar, V. / Soden, P.E. / Haynes, A. / Vappiani, J. / Tough, D.F. / Taylor, S. / Dawson, S.J. / Bantscheff, M. / Lindon, M. / Drewes, G. / Demont, E.H. / Daniels, D.L. / Grandi, P. / Prinjha, R.K. / Dawson, M.A.
History
DepositionSep 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0684
Polymers13,4321
Non-polymers6363
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint3 kcal/mol
Surface area6750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.974, 52.713, 32.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bromodomain-containing protein 2 / BRD2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13432.462 Da / Num. of mol.: 1
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: Chemical ChemComp-LWB / 4-[2-(methoxymethyl)-1-[(1~{R})-1-phenylethyl]-8-[[(3~{S})-pyrrolidin-3-yl]methoxy]imidazo[4,5-c]quinolin-7-yl]-3,5-dimethyl-1,2-oxazole


Mass: 511.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H33N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% PEG 300, 0.1M MES buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: CCD / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→26.26 Å / Num. obs: 15926 / % possible obs: 95.6 % / Redundancy: 2.6 % / CC1/2: 0.991 / Net I/σ(I): 21.3
Reflection shellResolution: 1.6→1.69 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1752 / CC1/2: 0.603

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.601→26.26 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.747 / SU ML: 0.06 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1913 821 5.194 %
Rwork0.1673 --
all0.169 --
obs-15807 94.778 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.519 Å2
Baniso -1Baniso -2Baniso -3
1--0.189 Å2-0 Å2-0 Å2
2---0.285 Å20 Å2
3---0.474 Å2
Refinement stepCycle: LAST / Resolution: 1.601→26.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 46 172 1128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.013996
X-RAY DIFFRACTIONr_bond_other_d0.0010.017906
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.6441344
X-RAY DIFFRACTIONr_angle_other_deg1.2611.642102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0825111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.092255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58715168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.188156
X-RAY DIFFRACTIONr_chiral_restr0.0650.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
X-RAY DIFFRACTIONr_nbd_refined0.20.2220
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.2819
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2461
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2355
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2132
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1230.27
X-RAY DIFFRACTIONr_nbd_other0.1090.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.227
X-RAY DIFFRACTIONr_mcbond_it1.0472.413445
X-RAY DIFFRACTIONr_mcbond_other1.0372.399443
X-RAY DIFFRACTIONr_mcangle_it1.7545.404555
X-RAY DIFFRACTIONr_mcangle_other1.7555.419556
X-RAY DIFFRACTIONr_scbond_it1.8362.872551
X-RAY DIFFRACTIONr_scbond_other1.8352.873552
X-RAY DIFFRACTIONr_scangle_it3.046.241789
X-RAY DIFFRACTIONr_scangle_other3.0386.244790
X-RAY DIFFRACTIONr_lrange_it7.23724.8291206
X-RAY DIFFRACTIONr_lrange_other6.82623.321149
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.601-1.6420.251410.2537460.25311880.9090.86966.24580.231
1.642-1.6870.271430.2579120.25811910.8430.84480.18470.225
1.687-1.7360.256520.210390.20211140.8410.88997.93540.18
1.736-1.7890.235530.20310660.20411300.9140.9299.02660.18
1.789-1.8480.224460.18110240.18210770.9020.93499.350.155
1.848-1.9120.197570.1799730.1810390.9350.94299.13380.151
1.912-1.9840.192430.1599720.1610230.930.95599.2180.136
1.984-2.0640.186510.1519040.1539710.9640.9698.35220.125
2.064-2.1560.184490.1598940.169500.9480.95999.26320.133
2.156-2.260.194550.158260.1528880.9520.96499.21170.12
2.26-2.3810.176460.1458160.1478670.9540.96499.42330.112
2.381-2.5240.228490.1537430.1578050.9430.96398.38510.122
2.524-2.6970.191410.1457400.1487920.9550.96598.61110.116
2.697-2.9110.172300.1586770.1597140.9680.96599.01960.133
2.911-3.1840.195400.1676120.1696620.9540.96498.48940.143
3.184-3.5540.158390.1545790.1546250.9740.97198.880.136
3.554-4.0910.148280.1615070.165420.9790.97398.70850.152
4.091-4.9810.196240.1554300.1574620.970.97698.26840.149
4.981-6.9210.181190.1753420.1753860.9640.96993.52330.167
6.921-26.3570.22150.2161840.2162460.9690.95780.89430.217

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