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- PDB-5xhk: Crystal structure of the BRD2-BD2 in complex with phenanthridinone -

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Basic information

Entry
Database: PDB / ID: 5xhk
TitleCrystal structure of the BRD2-BD2 in complex with phenanthridinone
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / bromodomain / BET family / BRD2 / Phenanthridinone
Function / homology
Function and homology information


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 / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...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 / 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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
METHOXYETHANE / phenanthridin-6(5H)-one / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsPadmanabhan, B. / Mathur, S. / Tripathi, S. / Deshmukh, P.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science and Technology (DST)-SERB India
Department of Biotechnology India
Citation
Journal: J. Biomol. Struct. Dyn. / Year: 2018
Title: Insights into the crystal structure of BRD2-BD2 - phenanthridinone complex and theoretical studies on phenanthridinone analogs.
Authors: Mathur, S. / Deshmukh, P. / Tripathi, S. / Marimuthu, P. / Padmanabhan, B.
#1: Journal: PLoS ONE / Year: 2016
Title: A Novel Phenanthridionone Based Scaffold As a Potential Inhibitor of the BRD2 Bromodomain: Crystal Structure of the Complex.
Authors: Tripathi, S. / Mathur, S. / Deshmukh, P. / Manjula, R. / Padmanabhan, B.
History
DepositionApr 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8465
Polymers13,4061
Non-polymers4404
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-3 kcal/mol
Surface area7040 Å2
Unit cell
Length a, b, c (Å)32.040, 52.510, 71.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-725-

HOH

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Components

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


Mass: 13406.319 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 348-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-2ME / METHOXYETHANE


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-LDR / phenanthridin-6(5H)-one


Mass: 195.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.07 % / Description: Thick plates.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG MME 2000, 10% Glycerol, Tris-Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2016
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.28→42.296 Å / Num. obs: 25998 / % possible obs: 83.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 9.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.032 / Rrim(I) all: 0.063 / Net I/av σ(I): 8.1 / Net I/σ(I): 11.7
Reflection shellResolution: 1.28→1.35 Å / Redundancy: 3 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.89 / Rpim(I) all: 0.192 / Rrim(I) all: 0.351 / Rsym value: 0.291 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IG6

5ig6


Resolution: 1.28→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.478 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.06
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 1280 4.9 %RANDOM
Rwork0.157 ---
obs0.1587 24672 82.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 44.45 Å2 / Biso mean: 13.542 Å2 / Biso min: 4.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0 Å2-0 Å2
2---0.38 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1.28→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 46 211 1198
Biso mean--17.66 24.98 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191090
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.9881479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4995134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63223.51954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27115191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.602157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021854
X-RAY DIFFRACTIONr_rigid_bond_restr1.20731090
X-RAY DIFFRACTIONr_sphericity_free14.41567
X-RAY DIFFRACTIONr_sphericity_bonded5.74851195
LS refinement shellResolution: 1.284→1.317 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 91 -
Rwork0.212 1882 -
all-1973 -
obs--87.3 %

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