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- PDB-4z93: BRD4 bromodomain 2 in complex with gamma-carboline-containing com... -

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Basic information

Entry
Database: PDB / ID: 4z93
TitleBRD4 bromodomain 2 in complex with gamma-carboline-containing compound, number 18.
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / Bromodomain
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 / chromatin / 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-4LD / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsMeagher, J.L. / Stuckey, J.A.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structure-Based Design of gamma-Carboline Analogues as Potent and Specific BET Bromodomain Inhibitors.
Authors: Ran, X. / Zhao, Y. / Liu, L. / Bai, L. / Yang, C.Y. / Zhou, B. / Meagher, J.L. / Chinnaswamy, K. / Stuckey, J.A. / Wang, S.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Experimental preparation / Structure summary
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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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)13,7353
Polymers13,2591
Non-polymers4762
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.862, 72.696, 32.115
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 4 / Protein HUNK1


Mass: 13259.451 Da / Num. of mol.: 1 / Fragment: bromodomain 2 (UNP residues 349-460)
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-4LD / 1-(3-cyclopropyl-5-methyl-1H-pyrazol-4-yl)-7-(3,5-dimethyl-1,2-oxazol-4-yl)-8-methoxy-5H-pyrido[4,3-b]indole


Mass: 413.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N5O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Peg 400, Imidizole, ATP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 32674 / % possible obs: 98.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 15.52 Å2 / Rmerge(I) obs: 0.045 / Χ2: 1.182 / Net I/av σ(I): 39.804 / Net I/σ(I): 13.9 / Num. measured all: 202248
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.27-1.296.10.32615610.73896.7
1.29-1.326.10.2816010.79799.5
1.32-1.346.20.24215850.80396.3
1.34-1.376.20.20915990.87999.9
1.37-1.46.20.17816230.85997.3
1.4-1.436.20.15515890.92499.8
1.43-1.476.20.13815940.98298
1.47-1.516.30.11916231.055100
1.51-1.556.30.10116191.23198.6
1.55-1.66.20.09516271.34799.9
1.6-1.666.30.08416371.37799.1
1.66-1.726.30.07516141.32199.4
1.72-1.86.30.06416531.27599.6
1.8-1.96.30.06216541.38999.8
1.9-2.026.20.05916401.63599.8
2.02-2.176.20.05516471.74799.9
2.17-2.396.30.04616611.46299.8
2.39-2.746.20.03916901.30499.8
2.74-3.456.20.03617141.15499.9
3.45-505.50.03617431.2796.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OUO

2ouo


Resolution: 1.27→29.77 Å / Cor.coef. Fo:Fc: 0.9675 / Cor.coef. Fo:Fc free: 0.9604 / SU R Cruickshank DPI: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.04 / SU Rfree Blow DPI: 0.044 / SU Rfree Cruickshank DPI: 0.043
RfactorNum. reflection% reflectionSelection details
Rfree0.1845 1649 5.08 %RANDOM
Rwork0.1555 ---
obs0.1569 32482 98.97 %-
Displacement parametersBiso max: 70.06 Å2 / Biso mean: 19.39 Å2 / Biso min: 8.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.7705 Å20 Å20 Å2
2--2.8781 Å20 Å2
3----1.1076 Å2
Refine analyzeLuzzati coordinate error obs: 0.142 Å
Refinement stepCycle: final / Resolution: 1.27→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 71 119 1099
Biso mean--21.23 31.16 -
Num. residues----112
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d521SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes23HARMONIC2
X-RAY DIFFRACTIONt_gen_planes323HARMONIC5
X-RAY DIFFRACTIONt_it1898HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion117SEMIHARMONIC5
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_contact2139SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1898HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3418HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion4.04
X-RAY DIFFRACTIONt_other_torsion2.75
LS refinement shellResolution: 1.27→1.31 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.1944 158 5.44 %
Rwork0.1627 2748 -
all0.1644 2906 -
obs--98.97 %
Refinement TLS params.Method: refined / Origin x: 10.1121 Å / Origin y: 2.5701 Å / Origin z: 0.4838 Å
111213212223313233
T-0.0152 Å2-0.0018 Å2-0.007 Å2--0.0194 Å20.0017 Å2---0.0246 Å2
L0.6145 °2-0.0107 °20.0829 °2-1.0676 °2-0.0874 °2--0.4554 °2
S0.0046 Å °0.0153 Å °-0.0335 Å °-0.0257 Å °-0.0033 Å °-0.0021 Å °-0.0167 Å °0.041 Å °-0.0013 Å °
Refinement TLS groupSelection details: { A|* }

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