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- PDB-6hdo: Crystal structure of human ATAD2 bromodomain in complex with 8-((... -

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Basic information

Entry
Database: PDB / ID: 6hdo
TitleCrystal structure of human ATAD2 bromodomain in complex with 8-(((1R,2R,3R,5S)-2-(2-(1,1-dioxidotetrahydro-2H-thiopyran-4-yl)ethyl)-8-azabicyclo[3.2.1]octan-3-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)quinolin-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-FZH / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.61 Å
AuthorsChung, C.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Aiming to Miss a Moving Target: Bromo and Extra Terminal Domain (BET) Selectivity in Constrained ATAD2 Inhibitors.
Authors: Bamborough, P. / Chung, C.W. / Furze, R.C. / Grandi, P. / Michon, A.M. / Watson, R.J. / Mitchell, D.J. / Barnett, H. / Prinjha, R.K. / Rau, C. / Sheppard, R.J. / Werner, T. / Demont, E.H.
History
DepositionAug 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ATPase family AAA domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3046
Polymers15,4541
Non-polymers8515
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Ligand binding characterised by biophysical methods
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-11 kcal/mol
Surface area8180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.254, 79.254, 135.033
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-1455-

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
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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FZH / 8-[[(1~{S},2~{R},3~{R},5~{R})-2-[2-[1,1-bis(oxidanylidene)thian-4-yl]ethyl]-8-azabicyclo[3.2.1]octan-3-yl]amino]-3-methyl-5-(5-methylpyridin-3-yl)-1~{H}-quinolin-2-one


Mass: 534.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H38N4O3S
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.96 Å3/Da / Density % sol: 68.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.1M trisHCl pH 7.0-8.0, 1.2-1.5M ammonium sulphate and 20-25% PEG3350
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.61→135.03 Å / Num. obs: 8153 / % possible obs: 99.6 % / Redundancy: 10.3 % / Net I/σ(I): 20.8
Reflection shellResolution: 2.61→2.75 Å / Redundancy: 10.7 % / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
RefinementResolution: 2.61→37.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 24.134 / SU ML: 0.555 / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23194 374 4.6 %RANDOM
Rwork0.18427 ---
obs0.18646 7735 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.947 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 2.61→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 56 180 1313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191152
X-RAY DIFFRACTIONr_bond_other_d0.0070.021095
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9731561
X-RAY DIFFRACTIONr_angle_other_deg0.95632522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45123.560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00515203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6871513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.050.0211249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02252
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_it5.9086.027519
X-RAY DIFFRACTIONr_mcbond_other5.7256.017518
X-RAY DIFFRACTIONr_mcangle_it8.04913.497647
X-RAY DIFFRACTIONr_mcangle_other8.04313.522648
X-RAY DIFFRACTIONr_scbond_it7.8316.883630
X-RAY DIFFRACTIONr_scbond_other7.7416.842624
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.18114.93902
X-RAY DIFFRACTIONr_long_range_B_refined12.26127.7261509
X-RAY DIFFRACTIONr_long_range_B_other12.10227.4451433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.613→2.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 33 -
Rwork0.217 545 -
obs--99.83 %

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