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- PDB-6ajx: Crystal structure of BRD4 in complex with isoliquiritigenin in th... -

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Basic information

Entry
Database: PDB / ID: 6ajx
TitleCrystal structure of BRD4 in complex with isoliquiritigenin in the absence of DMSO
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / bromodomain / brd4 / inhibitor / isoliquiritigenin
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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 II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / 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
2',4,4'-TRIHYDROXYCHALCONE / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.887 Å
AuthorsYokoyama, T. / Matsumoto, K. / Nabeshima, Y. / Mizuguchi, M.
CitationJournal: Febs J. / Year: 2019
Title: Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.
Authors: Yokoyama, T. / Matsumoto, K. / Ostermann, A. / Schrader, T.E. / Nabeshima, Y. / Mizuguchi, M.
History
DepositionAug 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4634
Polymers16,1611
Non-polymers3023
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-15 kcal/mol
Surface area8080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.830, 46.875, 78.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 16160.562 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 (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-HCC / 2',4,4'-TRIHYDROXYCHALCONE


Mass: 256.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 1.87 Å3/Da / Density % sol: 34.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4M sodium formate, 0.1M tris-HCl pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.887→40.3 Å / Num. obs: 10088 / % possible obs: 98.4 % / Redundancy: 5.8 % / Rpim(I) all: 0.03 / Net I/σ(I): 17.1
Reflection shellResolution: 1.89→1.95 Å / Rpim(I) all: 0.211

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Processing

Software
NameVersionClassification
PHENIX(1.12-2829_1069: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 1.887→30.289 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.09
RfactorNum. reflection% reflection
Rfree0.2366 504 5 %
Rwork0.2044 --
obs0.2061 10075 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.887→30.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 21 43 1154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061156
X-RAY DIFFRACTIONf_angle_d0.811577
X-RAY DIFFRACTIONf_dihedral_angle_d21.481446
X-RAY DIFFRACTIONf_chiral_restr0.069165
X-RAY DIFFRACTIONf_plane_restr0.006203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8875-2.07740.31221240.24082348X-RAY DIFFRACTION99
2.0774-2.37790.29711250.22372393X-RAY DIFFRACTION100
2.3779-2.99550.27491260.23662396X-RAY DIFFRACTION99
2.9955-30.29240.19521290.182434X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -10.5502 Å / Origin y: -1.8287 Å / Origin z: 8.5479 Å
111213212223313233
T0.2753 Å2-0.0445 Å20.0295 Å2-0.2583 Å2-0.0124 Å2--0.2449 Å2
L1.815 °2-0.5971 °2-0.146 °2-4.7993 °2-0.1588 °2--2.3642 °2
S0.023 Å °0.0048 Å °0.0422 Å °-0.1808 Å °0.0492 Å °-0.201 Å °-0.2267 Å °0.0943 Å °-0.064 Å °
Refinement TLS groupSelection details: (chain A and resid 37:166)

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