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- PDB-6hi6: The ATAD2 bromodomain in complex with compound 9 -

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Basic information

Entry
Database: PDB / ID: 6hi6
TitleThe ATAD2 bromodomain in complex with compound 9
ComponentsATPase family AAA domain-containing protein 2
KeywordsCYTOSOLIC PROTEIN / Bromodomain / ATAD2 / inhibitor / complex
Function / homology
Function and homology information


nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome ...nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / 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) / Bromodomain-like / Histone Acetyltransferase; Chain A / ATPase, AAA-type, core / 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) / Bromodomain-like / Histone Acetyltransferase; Chain A / ATPase, AAA-type, core / 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-G5Z / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsSledz, P. / Caflisch, A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers.
Authors: Dolbois, A. / Batiste, L. / Wiedmer, L. / Dong, J. / Brutsch, M. / Huang, D. / Deerain, N.M. / Spiliotopoulos, D. / Cheng-Sanchez, I. / Laul, E. / Nevado, C. / Sledz, P. / Caflisch, A.
History
DepositionAug 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: ATPase family AAA domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2265
Polymers15,4541
Non-polymers7734
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-19 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.340, 79.340, 136.212
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-1339-

HOH

21A-1438-

HOH

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Components

#1: Protein ATPase family AAA domain-containing protein 2 / Bromodomain of ATAD2


Mass: 15453.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-G5Z / (2~{R})-2-azanyl-~{N}-(4-ethanoyl-5-pyridin-3-yl-1,3-thiazol-2-yl)propanamide


Mass: 290.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14N4O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 4 Å3/Da / Density % sol: 69.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.64→48.371 Å / Num. obs: 58570 / % possible obs: 99.5 % / Redundancy: 10.34 % / CC1/2: 1 / Rrim(I) all: 0.071 / Net I/σ(I): 19.33
Reflection shellResolution: 1.64→1.74 Å / Redundancy: 9.45 % / Num. unique obs: 9239 / CC1/2: 0.471 / Rrim(I) all: 2.025 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F36

5f36


Resolution: 1.64→48.371 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.99
RfactorNum. reflection% reflection
Rfree0.2347 2949 5.04 %
Rwork0.2107 --
obs0.212 58497 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.64→48.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 37 141 1213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081091
X-RAY DIFFRACTIONf_angle_d1.1111478
X-RAY DIFFRACTIONf_dihedral_angle_d1.991929
X-RAY DIFFRACTIONf_chiral_restr0.041167
X-RAY DIFFRACTIONf_plane_restr0.004192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6402-1.66710.29511260.3242420X-RAY DIFFRACTION90
1.6671-1.69590.33371400.29872658X-RAY DIFFRACTION100
1.6959-1.72670.31191410.29572668X-RAY DIFFRACTION100
1.7267-1.75990.32171440.29652652X-RAY DIFFRACTION100
1.7599-1.79580.29271380.29022628X-RAY DIFFRACTION100
1.7958-1.83490.28541420.28712661X-RAY DIFFRACTION100
1.8349-1.87760.32831450.27782650X-RAY DIFFRACTION100
1.8776-1.92450.29971420.24782654X-RAY DIFFRACTION100
1.9245-1.97660.31711400.22812668X-RAY DIFFRACTION100
1.9766-2.03470.29941370.21732673X-RAY DIFFRACTION100
2.0347-2.10040.20361430.21422652X-RAY DIFFRACTION100
2.1004-2.17550.18991410.20712643X-RAY DIFFRACTION100
2.1755-2.26260.27281380.20542662X-RAY DIFFRACTION100
2.2626-2.36560.27521390.2062653X-RAY DIFFRACTION100
2.3656-2.49030.24261420.20972655X-RAY DIFFRACTION100
2.4903-2.64630.21051360.21212667X-RAY DIFFRACTION100
2.6463-2.85060.2611390.21532661X-RAY DIFFRACTION100
2.8506-3.13740.24871450.22092641X-RAY DIFFRACTION100
3.1374-3.59130.19321370.18482678X-RAY DIFFRACTION100
3.5913-4.52410.18511490.17992636X-RAY DIFFRACTION100
4.5241-48.39150.24461450.20792668X-RAY DIFFRACTION100

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