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- PDB-5lj0: Crystal structure of human ATAD2 bromodomain in complex with 8-((... -

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Basic information

Entry
Database: PDB / ID: 5lj0
TitleCrystal structure of human ATAD2 bromodomain in complex with 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one
ComponentsATPase family AAA domain-containing protein 2
KeywordsTRANSCRIPTION / INHIBITOR / ATAD2 / BROMODOMAIN / EPIGENETICS / ATPase family AAA domain-containing protein 2
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus
Similarity search - Function
ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain ...ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Chem-6XX / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.82 Å
AuthorsChung, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: A Chemical Probe for the ATAD2 Bromodomain.
Authors: Bamborough, P. / Chung, C.W. / Demont, E.H. / Furze, R.C. / Bannister, A.J. / Che, K.H. / Diallo, H. / Douault, C. / Grandi, P. / Kouzarides, T. / Michon, A.M. / Mitchell, D.J. / Prinjha, R. ...Authors: Bamborough, P. / Chung, C.W. / Demont, E.H. / Furze, R.C. / Bannister, A.J. / Che, K.H. / Diallo, H. / Douault, C. / Grandi, P. / Kouzarides, T. / Michon, A.M. / Mitchell, D.J. / Prinjha, R.K. / Rau, C. / Robson, S. / Sheppard, R.J. / Upton, R. / Watson, R.J.
History
DepositionJul 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATPase family AAA domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3257
Polymers15,4541
Non-polymers8726
Water4,486249
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-0 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.158, 79.158, 135.857
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1359-

HOH

21A-1506-

HOH

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Components

#1: Protein ATPase family AAA domain-containing protein 2 / AAA nuclear coregulator cancer-associated protein / ANCCA


Mass: 15453.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SM first two residues are residual after cleavage of the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18, EC: 3.6.1.3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-6XX / 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one


Mass: 527.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H35F2N5O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 3.98 Å3/Da / Density % sol: 69.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M trisHCl, pH 7.0-8.0, 1.2-1.5M ammonium sulphate, 20-25% PEG3350,277K
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95373 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.82→135.86 Å / Num. obs: 23289 / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 19.3
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
RefinementResolution: 1.82→68.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.419 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18256 1192 5.1 %RANDOM
Rwork0.17378 ---
obs0.17424 22036 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.982 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.82→68.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 59 249 1392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191196
X-RAY DIFFRACTIONr_bond_other_d0.0030.021164
X-RAY DIFFRACTIONr_angle_refined_deg0.9491.9871618
X-RAY DIFFRACTIONr_angle_other_deg0.74232682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1835137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50223.28164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01715221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8581515
X-RAY DIFFRACTIONr_chiral_restr0.0580.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211294
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02267
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2942.895527
X-RAY DIFFRACTIONr_mcbond_other1.2842.885526
X-RAY DIFFRACTIONr_mcangle_it2.1566.475659
X-RAY DIFFRACTIONr_mcangle_other2.166.491660
X-RAY DIFFRACTIONr_scbond_it1.9913.426668
X-RAY DIFFRACTIONr_scbond_other1.9863.413664
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4027.398949
X-RAY DIFFRACTIONr_long_range_B_refined8.20415.821699
X-RAY DIFFRACTIONr_long_range_B_other8.20415.8191699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.822→1.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 74 -
Rwork0.205 1601 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -12.5882 Å / Origin y: 40.853 Å / Origin z: 3.4195 Å
111213212223313233
T0.0155 Å2-0.023 Å20.0026 Å2-0.0917 Å2-0.0356 Å2--0.027 Å2
L2.3605 °2-0.1356 °2-0.6309 °2-0.0232 °20.1179 °2--0.8138 °2
S-0.0507 Å °-0.2264 Å °0.0951 Å °-0.003 Å °0.0334 Å °-0.0082 Å °0.0226 Å °0.0313 Å °0.0174 Å °

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