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- PDB-5m3a: Crystal structure of BRD4 BROMODOMAIN 1 IN COMPLEX WITH LIGAND 2 -

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Basic information

Entry
Database: PDB / ID: 5m3a
TitleCrystal structure of BRD4 BROMODOMAIN 1 IN COMPLEX WITH LIGAND 2
ComponentsBromodomain-containing protein 4BRD4
KeywordsTRANSCRIPTION / BROMODOMAIN / BRD4 BD1 / EPIGENETIC / HISTONE READER
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 / 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 protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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
Chem-7E7 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKessler, D. / Mayer, M. / Engelhardt, H. / Wolkerstorfer, B. / Geist, L.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Direct NMR Probing of Hydration Shells of Protein Ligand Interfaces and Its Application to Drug Design.
Authors: Geist, L. / Mayer, M. / Cockcroft, X.L. / Wolkerstorfer, B. / Kessler, D. / Engelhardt, H. / McConnell, D.B. / Konrat, R.
History
DepositionOct 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5304
Polymers15,0991
Non-polymers4303
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint6 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.260, 44.180, 78.490
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 / BRD4 / Protein HUNK1


Mass: 15099.380 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BIND CRYSTAL_ID 1009192 / Source: (natural) Homo sapiens (human) / Fragment: BRD4 bromodomain 1 corresponding to pdb id 2OSS / References: UniProt: O60885
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-7E7 / 3-methyl-6-(1-methyl-5-phenoxy-pyrazol-4-yl)-[1,2,4]triazolo[4,3-b]pyridazine


Mass: 306.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N6O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1M HEPES PEG3350 22% Di-Sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→44.2 Å / Num. obs: 13114 / % possible obs: 81.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 16.13 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.034 / Net I/σ(I): 18.2
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.59 / % possible all: 27.2

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OSS

2oss


Resolution: 1.65→38.5 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.162 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.214 628 4.81 %RANDOM
Rwork0.187 ---
obs0.188 13069 80.7 %-
Displacement parametersBiso mean: 18.09 Å2
Baniso -1Baniso -2Baniso -3
1--4.0681 Å20 Å20 Å2
2--2.0037 Å20 Å2
3---2.0645 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.65→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 31 211 1304
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081147HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.881566HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d400SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes155HARMONIC5
X-RAY DIFFRACTIONt_it1147HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.34
X-RAY DIFFRACTIONt_other_torsion16.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion146SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1603SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.283 -5.17 %
Rwork0.272 1008 -
all0.272 1063 -
obs--32.57 %
Refinement TLS params.Method: refined / Origin x: 25.3403 Å / Origin y: 40.6361 Å / Origin z: 8.6856 Å
111213212223313233
T-0.0195 Å20.0002 Å20.0093 Å2--0.034 Å2-0.0121 Å2---0.0319 Å2
L0.5304 °20.1041 °2-0.0914 °2-0.6561 °2-0.195 °2--1.2143 °2
S0.0016 Å °-0.0241 Å °-0.0079 Å °0.0348 Å °0.0055 Å °0.0123 Å °0.0698 Å °-0.0002 Å °-0.0071 Å °
Refinement TLS groupSelection details: { A|* }

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